Data Intake
| Index | stub | file | data_type | taxon_string | translation_table |
|---|---|---|---|---|---|
| 0 | KX808498-truncated | KX808498-truncated.gb | GenBank | Caulerpa_cliftonii_HV03798 | 11 |
| 1 | KY509313-truncated | KY509313-truncated.gb | GenBank | Avrainvillea_mazei_HV02664 | 11 |
| 2 | MH591083-truncated | MH591083-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 3 | MH591084-truncated | MH591084-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 4 | MH591085-truncated | MH591085-truncated.gb | GenBank | Flabellia_petiolata_HV01202 | 11 |
| 5 | NC_026795-truncated | NC_026795-truncated.txt | GenBank | Bryopsis_plumosa_WEST4718 | 11 |
| 6 | KY819064-truncated-cds | KY819064-truncated.cds.fasta | CDS | Chlorodesmis_fastigiata_HV03865 | 11 |
Orthofinder
| Orthogroup | KX808498-truncated.protein | KY509313-truncated.protein | KY819064-truncated-cds.protein | MH591083-truncated.protein | MH591084-truncated.protein | MH591085-truncated.protein | NC_026795-truncated.protein |
|---|---|---|---|---|---|---|---|
| OG0000000 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|28|psbE | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|6|psbE, Avrainvillea_mazei_HV02664|KY509313-truncated.gb|7|orf100 | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|5|KY819064.1|psbE | — | — | Flabellia_petiolata_HV01202|MH591085-truncated.gb|0|psbE | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|5|psbE |
| OG0000001 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|22|rpl23 | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|3|rpl23 | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|1|KY819064.1|rpl23 | — | Flabellia_petiolata_HV01202|MH591084-truncated.gb|1|rpl23 | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|1|rpl23 |
| OG0000002 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|23|petA | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|0|petA | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|0|KY819064.1|petA | — | Flabellia_petiolata_HV01202|MH591084-truncated.gb|0|petA | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|0|petA |
| OG0000003 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|24|psaI | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|1|psaI | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|2|KY819064.1|psaI | Flabellia_petiolata_HV01202|MH591083-truncated.gb|1|psaI | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|2|psaI |
| OG0000004 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|26|petG | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|2|petG | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|3|KY819064.1|petG | Flabellia_petiolata_HV01202|MH591083-truncated.gb|0|petG | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|3|petG |
| OG0000005 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|27|rbcL | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|4|rbcL | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|4|KY819064.1|rbcL | Flabellia_petiolata_HV01202|MH591083-truncated.gb|2|rbcL | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|4|rbcL |
| OG0000006 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|29|rps18, Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|30|orf179 | Avrainvillea_mazei_HV02664|KY509313-truncated.gb|5|rps18 | Chlorodesmis_fastigiata_HV03865|KY819064-truncated.cds.fasta|6|KY819064.1|rps18 | — | — | — | Bryopsis_plumosa_WEST4718|NC_026795-truncated.txt|6|rps18 |
| Orthogroup | KX808498-truncated.protein | KY509313-truncated.protein | KY819064-truncated-cds.protein | MH591083-truncated.protein | MH591084-truncated.protein | MH591085-truncated.protein | NC_026795-truncated.protein |
|---|---|---|---|---|---|---|---|
| OG0000007 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|0|rps9 | — | — | — | — | — | — |
| OG0000008 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|1|rpoC1 | — | — | — | — | — | — |
| OG0000009 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|2|rpoC2 | — | — | — | — | — | — |
| OG0000010 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|3|psaB | — | — | — | — | — | — |
| OG0000011 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|4|psbZ | — | — | — | — | — | — |
| OG0000012 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|5|orf180 | — | — | — | — | — | — |
| OG0000013 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|6|orf116 | — | — | — | — | — | — |
| OG0000014 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|7|orf144 | — | — | — | — | — | — |
| OG0000015 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|8|orf519 | — | — | — | — | — | — |
| OG0000016 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|9|psbA | — | — | — | — | — | — |
| OG0000017 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|10|orf128 | — | — | — | — | — | — |
| OG0000018 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|11|rpoA | — | — | — | — | — | — |
| OG0000019 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|12|rps11 | — | — | — | — | — | — |
| OG0000020 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|13|rpl36 | — | — | — | — | — | — |
| OG0000021 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|14|infA | — | — | — | — | — | — |
| OG0000022 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|15|rps8 | — | — | — | — | — | — |
| OG0000023 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|16|rpl5 | — | — | — | — | — | — |
| OG0000024 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|17|rpl14 | — | — | — | — | — | — |
| OG0000025 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|18|rpl16 | — | — | — | — | — | — |
| OG0000026 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|19|rps3 | — | — | — | — | — | — |
| OG0000027 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|20|rps19 | — | — | — | — | — | — |
| OG0000028 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|21|rpl2 | — | — | — | — | — | — |
| OG0000029 | Caulerpa_cliftonii_HV03798|KX808498-truncated.gb|25|ycf20 | — | — | — | — | — | — |
| Input | KX808498-truncated.protein | KY509313-truncated.protein | KY819064-truncated-cds.protein | MH591083-truncated.protein | MH591084-truncated.protein | MH591085-truncated.protein | NC_026795-truncated.protein |
|---|---|---|---|---|---|---|---|
| KX808498-truncated.protein | 7 | 7 | 7 | 3 | 2 | 1 | 7 |
| KY509313-truncated.protein | 7 | 7 | 7 | 3 | 2 | 1 | 7 |
| KY819064-truncated-cds.protein | 7 | 7 | 7 | 3 | 2 | 1 | 7 |
| MH591083-truncated.protein | 3 | 3 | 3 | 3 | 0 | 0 | 3 |
| MH591084-truncated.protein | 2 | 2 | 2 | 0 | 2 | 0 | 2 |
| MH591085-truncated.protein | 1 | 1 | 1 | 0 | 0 | 1 | 1 |
| NC_026795-truncated.protein | 7 | 7 | 7 | 3 | 2 | 1 | 7 |
results/orthofinder/output/Orthogroup_Sequences/OG0000001.fa results/orthofinder/output/Orthogroup_Sequences/OG0000002.fa results/orthofinder/output/Orthogroup_Sequences/OG0000003.fa results/orthofinder/output/Orthogroup_Sequences/OG0000004.fa results/orthofinder/output/Orthogroup_Sequences/OG0000005.fa
results/orthofinder/orthosnap/OG0000000/OG0000000_orthosnap_0.fa
Alignment
results/alignment/trimmed_protein/OG0000005.trimmed.protein.alignment.fa results/alignment/trimmed_protein/OG0000002.trimmed.protein.alignment.fa
Supermatrix
General Characteristics ======================= 5 Number of taxa 795 Alignment length 59 Parsimony informative sites 59 Variable sites 716 Constant sites Character Frequencies ===================== Y 146 W 42 V 283 T 199 S 159 R 181 Q 193 P 224 N 185 M 64 L 347 K 247 I 254 H 81 G 342 F 192 E 226 D 193 C 64 A 306 - 47
IQ-TREE 2.2.0.3 COVID-edition built Aug 2 2022
Input file name: results/supermatrix/supermatrix.protein.fa
Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates)
Random seed number: 310712
REFERENCES
----------
To cite IQ-TREE please use:
Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf,
Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020)
IQ-TREE 2: New models and efficient methods for phylogenetic inference
in the genomic era. Mol. Biol. Evol., in press.
https://doi.org/10.1093/molbev/msaa015
To cite ModelFinder please use:
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler,
and Lars S Jermiin (2017) ModelFinder: Fast model selection for
accurate phylogenetic estimates. Nature Methods, 14:587–589.
https://doi.org/10.1038/nmeth.4285
Since you used ultrafast bootstrap (UFBoot) please also cite:
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh,
and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap
approximation. Mol. Biol. Evol., 35:518–522.
https://doi.org/10.1093/molbev/msx281
SEQUENCE ALIGNMENT
------------------
Input data: 5 sequences with 795 amino-acid sites
Number of constant sites: 568 (= 71.4465% of all sites)
Number of invariant (constant or ambiguous constant) sites: 568 (= 71.4465% of all sites)
Number of parsimony informative sites: 59
Number of distinct site patterns: 233
ModelFinder
-----------
Best-fit model according to BIC: cpREV+G4
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
cpREV+G4 -4264.235 8544.470 + 0.28 8544.653 + 0.305 8581.896 + 0.758
cpREV+I+G4 -4262.935 8543.870 + 0.378 8544.100 + 0.403 8585.975 + 0.0987
LG+G4 -4266.340 8548.680 - 0.0341 8548.863 - 0.0372 8586.107 + 0.0924
LG+I+G4 -4263.605 8545.210 + 0.193 8545.439 + 0.206 8587.315 + 0.0505
Q.pfam+G4 -4274.081 8564.163 - 1.48e-05 8564.346 - 1.62e-05 8601.590 - 4.01e-05
LG+I -4274.116 8564.233 - 1.43e-05 8564.416 - 1.56e-05 8601.659 - 3.88e-05
Q.pfam+I+G4 -4271.452 8560.904 - 7.56e-05 8561.133 - 8.06e-05 8603.009 - 1.97e-05
WAG+G4 -4276.694 8569.388 - 1.09e-06 8569.572 - 1.19e-06 8606.815 - 2.94e-06
WAG+I+G4 -4275.346 8568.692 - 1.54e-06 8568.921 - 1.64e-06 8610.797 - 4.02e-07
VT+G4 -4278.977 8573.953 - 1.11e-07 8574.136 - 1.21e-07 8611.380 - 3e-07
VT+I+G4 -4277.863 8573.727 - 1.24e-07 8573.956 - 1.32e-07 8615.832 - 3.24e-08
rtREV+G4 -4288.723 8593.447 - 6.49e-12 8593.630 - 7.07e-12 8630.874 - 1.76e-11
rtREV+I+G4 -4286.522 8591.044 - 2.16e-11 8591.273 - 2.3e-11 8633.149 - 5.63e-12
Q.plant+I+G4 -4286.649 8591.299 - 1.9e-11 8591.528 - 2.02e-11 8633.404 - 4.96e-12
JTTDCMut+G4 -4290.078 8596.156 - 1.67e-12 8596.339 - 1.82e-12 8633.583 - 4.53e-12
Blosum62+G4 -4290.417 8596.834 - 1.19e-12 8597.017 - 1.3e-12 8634.261 - 3.23e-12
JTTDCMut+I+G4 -4287.253 8592.507 - 1.04e-11 8592.736 - 1.11e-11 8634.612 - 2.71e-12
JTT+G4 -4290.924 8597.849 - 7.18e-13 8598.032 - 7.83e-13 8635.275 - 1.94e-12
Q.plant+G4 -4291.377 8598.753 - 4.57e-13 8598.937 - 4.98e-13 8636.180 - 1.24e-12
JTT+I+G4 -4288.113 8594.227 - 4.39e-12 8594.456 - 4.68e-12 8636.332 - 1.15e-12
Blosum62+I+G4 -4289.528 8597.055 - 1.07e-12 8597.284 - 1.14e-12 8639.160 - 2.79e-13
Q.yeast+I+G4 -4292.732 8603.464 - 4.33e-14 8603.693 - 4.62e-14 8645.569 - 1.13e-14
PMB+G4 -4296.492 8608.984 - 2.74e-15 8609.167 - 2.99e-15 8646.411 - 7.43e-15
Q.yeast+G4 -4296.496 8608.992 - 2.73e-15 8609.175 - 2.98e-15 8646.419 - 7.4e-15
PMB+I+G4 -4295.845 8609.691 - 1.93e-15 8609.920 - 2.05e-15 8651.796 - 5.03e-16
Q.insect+I+G4 -4299.971 8617.941 - 3.11e-17 8618.171 - 3.32e-17 8660.046 - 8.12e-18
Q.insect+G4 -4303.627 8623.254 - 2.18e-18 8623.437 - 2.38e-18 8660.681 - 5.92e-18
cpREV+F+G4 -4247.364 8548.727 - 0.0333 8550.698 - 0.0149 8675.042 - 4.5e-21
LG+F+G4 -4249.084 8552.168 - 0.00596 8554.139 - 0.00266 8678.483 - 8.06e-22
cpREV+F+I+G4 -4246.056 8548.113 - 0.0453 8550.233 - 0.0188 8679.106 - 5.9e-22
LG+F+I+G4 -4246.511 8549.022 - 0.0287 8551.142 - 0.0119 8680.016 - 3.75e-22
Dayhoff+G4 -4313.542 8643.085 - 1.08e-22 8643.268 - 1.18e-22 8680.512 - 2.92e-22
DCMut+G4 -4313.567 8643.135 - 1.05e-22 8643.318 - 1.15e-22 8680.561 - 2.85e-22
Dayhoff+I+G4 -4310.935 8639.869 - 5.39e-22 8640.099 - 5.74e-22 8681.974 - 1.41e-22
DCMut+I+G4 -4310.984 8639.968 - 5.13e-22 8640.197 - 5.46e-22 8682.073 - 1.34e-22
Q.pfam+F+G4 -4253.010 8560.020 - 0.000118 8561.991 - 5.25e-05 8686.335 - 1.59e-23
WAG+F+G4 -4253.474 8560.948 - 7.4e-05 8562.919 - 3.3e-05 8687.263 - 9.99e-24
Q.pfam+F+I+G4 -4250.465 8556.930 - 0.000551 8559.050 - 0.000228 8687.924 - 7.18e-24
mtZOA+F+I+G4 -4251.120 8558.239 - 0.000287 8560.359 - 0.000119 8689.233 - 3.73e-24
mtZOA+F+G4 -4255.408 8564.815 - 1.07e-05 8566.786 - 4.77e-06 8691.130 - 1.45e-24
WAG+F+I+G4 -4252.112 8560.224 - 0.000106 8562.344 - 4.4e-05 8691.217 - 1.38e-24
mtART+F+I+G4 -4253.942 8563.884 - 1.7e-05 8566.004 - 7.05e-06 8694.877 - 2.22e-25
mtInv+F+G4 -4257.685 8569.369 - 1.1e-06 8571.341 - 4.89e-07 8695.685 - 1.48e-25
mtInv+F+I+G4 -4254.766 8565.531 - 7.48e-06 8567.652 - 3.1e-06 8696.525 - 9.74e-26
mtART+F+G4 -4258.168 8570.336 - 6.77e-07 8572.308 - 3.02e-07 8696.652 - 9.14e-26
rtREV+F+G4 -4259.244 8572.489 - 2.31e-07 8574.460 - 1.03e-07 8698.804 - 3.12e-26
rtREV+F+I+G4 -4257.099 8570.198 - 7.25e-07 8572.318 - 3e-07 8701.192 - 9.45e-27
Q.yeast+F+I+G4 -4258.571 8573.141 - 1.66e-07 8575.261 - 6.89e-08 8704.135 - 2.17e-27
Q.yeast+F+G4 -4261.964 8577.929 - 1.52e-08 8579.900 - 6.78e-09 8704.244 - 2.05e-27
Q.plant+F+I+G4 -4261.841 8579.682 - 6.32e-09 8581.802 - 2.62e-09 8710.676 - 8.24e-29
Q.plant+F+G4 -4266.457 8586.915 - 1.7e-10 8588.886 - 7.58e-11 8713.230 - 2.3e-29
mtREV+F+G4 -4266.466 8586.932 - 1.69e-10 8588.903 - 7.51e-11 8713.247 - 2.28e-29
VT+F+G4 -4267.014 8588.028 - 9.74e-11 8589.999 - 4.34e-11 8714.343 - 1.32e-29
mtREV+F+I+G4 -4263.923 8583.846 - 7.88e-10 8585.966 - 3.26e-10 8714.839 - 1.03e-29
Q.insect+F+G4 -4268.562 8591.124 - 2.07e-11 8593.095 - 9.24e-12 8717.439 - 2.8e-30
Q.insect+F+I+G4 -4265.282 8586.563 - 2.03e-10 8588.683 - 8.39e-11 8717.557 - 2.64e-30
VT+F+I+G4 -4266.007 8588.013 - 9.81e-11 8590.133 - 4.06e-11 8719.007 - 1.28e-30
PMB+F+G4 -4272.250 8598.500 - 5.18e-13 8600.471 - 2.31e-13 8724.815 - 7.01e-32
HIVb+I+G4 -4332.623 8683.246 - 2.05e-31 8683.475 - 2.19e-31 8725.351 - 5.36e-32
JTTDCMut+F+G4 -4272.902 8599.804 - 2.7e-13 8601.775 - 1.2e-13 8726.119 - 3.65e-32
JTTDCMut+F+I+G4 -4270.101 8596.202 - 1.64e-12 8598.322 - 6.77e-13 8727.195 - 2.13e-32
Dayhoff+F+G4 -4273.453 8600.906 - 1.56e-13 8602.878 - 6.94e-14 8727.222 - 2.1e-32
DCMut+F+G4 -4273.485 8600.970 - 1.51e-13 8602.941 - 6.72e-14 8727.285 - 2.04e-32
JTT+F+G4 -4273.601 8601.202 - 1.34e-13 8603.173 - 5.99e-14 8727.517 - 1.81e-32
Dayhoff+F+I+G4 -4270.621 8597.242 - 9.72e-13 8599.362 - 4.03e-13 8728.235 - 1.27e-32
DCMut+F+I+G4 -4270.680 8597.360 - 9.17e-13 8599.480 - 3.8e-13 8728.353 - 1.19e-32
HIVb+G4 -4337.534 8691.069 - 4.11e-33 8691.252 - 4.48e-33 8728.495 - 1.11e-32
JTT+F+I+G4 -4270.827 8597.654 - 7.91e-13 8599.774 - 3.28e-13 8728.647 - 1.03e-32
PMB+F+I+G4 -4271.626 8599.252 - 3.56e-13 8601.372 - 1.47e-13 8730.246 - 4.64e-33
Blosum62+F+G4 -4276.695 8607.391 - 6.08e-15 8609.362 - 2.71e-15 8733.706 - 8.22e-34
mtMet+F+I+G4 -4273.719 8603.439 - 4.39e-14 8605.559 - 1.82e-14 8734.432 - 5.72e-34
mtMet+F+G4 -4277.978 8609.955 - 1.69e-15 8611.927 - 7.52e-16 8736.271 - 2.28e-34
Blosum62+F+I+G4 -4275.878 8607.755 - 5.07e-15 8609.875 - 2.1e-15 8738.749 - 6.6e-35
FLU+I+G4 -4341.240 8700.481 - 3.71e-35 8700.710 - 3.96e-35 8742.586 - 9.7e-36
FLU+G4 -4346.657 8709.314 - 4.48e-37 8709.497 - 4.89e-37 8746.741 - 1.21e-36
Q.mammal+I+G4 -4344.882 8707.764 - 9.73e-37 8707.993 - 1.04e-36 8749.869 - 2.54e-37
Q.bird+I+G4 -4345.555 8709.110 - 4.97e-37 8709.339 - 5.29e-37 8751.215 - 1.3e-37
Q.mammal+G4 -4350.388 8716.777 - 1.07e-38 8716.960 - 1.17e-38 8754.204 - 2.91e-38
Q.bird+G4 -4352.531 8721.063 - 1.26e-39 8721.246 - 1.37e-39 8758.490 - 3.41e-39
FLU+F+I+G4 -4295.811 8647.622 - 1.12e-23 8649.742 - 4.62e-24 8778.616 - 1.45e-43
FLU+F+G4 -4300.960 8655.921 - 1.76e-25 8657.892 - 7.85e-26 8782.236 - 2.38e-44
mtVer+F+I+G4 -4301.125 8658.250 - 5.5e-26 8660.370 - 2.28e-26 8789.243 - 7.16e-46
Q.mammal+F+I+G4 -4302.004 8660.008 - 2.28e-26 8662.128 - 9.45e-27 8791.002 - 2.97e-46
mtMAM+F+I+G4 -4302.137 8660.274 - 2e-26 8662.394 - 8.27e-27 8791.268 - 2.6e-46
HIVb+F+I+G4 -4302.523 8661.045 - 1.36e-26 8663.166 - 5.62e-27 8792.039 - 1.77e-46
HIVb+F+G4 -4307.488 8668.976 - 2.58e-28 8670.947 - 1.15e-28 8795.291 - 3.48e-47
Q.mammal+F+G4 -4307.577 8669.153 - 2.36e-28 8671.124 - 1.05e-28 8795.468 - 3.19e-47
mtVer+F+G4 -4308.190 8670.379 - 1.28e-28 8672.350 - 5.7e-29 8796.694 - 1.73e-47
mtMAM+F+G4 -4308.475 8670.949 - 9.6e-29 8672.921 - 4.28e-29 8797.265 - 1.3e-47
LG -4378.052 8770.104 - 2.83e-50 8770.246 - 3.15e-50 8802.852 - 7.94e-49
Q.bird+F+I+G4 -4311.654 8679.308 - 1.47e-30 8681.428 - 6.09e-31 8810.302 - 1.92e-50
Q.bird+F+G4 -4318.788 8691.576 - 3.19e-33 8693.547 - 1.42e-33 8817.891 - 4.31e-52
FLAVI+I+G4 -4392.585 8803.169 - 1.87e-57 8803.398 - 1.99e-57 8845.274 - 4.88e-58
FLAVI+G4 -4401.151 8818.302 - 9.66e-61 8818.486 - 1.05e-60 8855.729 - 2.62e-60
FLAVI+F+I+G4 -4334.743 8725.486 - 1.38e-40 8727.607 - 5.71e-41 8856.480 - 1.8e-60
FLAVI+F+G4 -4343.385 8740.771 - 6.62e-44 8742.742 - 2.95e-44 8867.086 - 8.95e-63
mtZOA+I+G4 -4408.102 8834.205 - 3.4e-64 8834.434 - 3.63e-64 8876.310 - 8.89e-65
mtZOA+G4 -4413.222 8842.444 - 5.53e-66 8842.627 - 6.03e-66 8879.870 - 1.5e-65
mtART+I+G4 -4433.667 8885.334 - 2.69e-75 8885.563 - 2.86e-75 8927.439 - 7.02e-76
mtART+G4 -4438.666 8893.332 - 4.93e-77 8893.515 - 5.37e-77 8930.759 - 1.33e-76
HIVw+I+G4 -4438.926 8895.852 - 1.4e-77 8896.081 - 1.49e-77 8937.957 - 3.65e-78
HIVw+G4 -4447.382 8910.764 - 8.08e-81 8910.947 - 8.81e-81 8948.191 - 2.19e-80
HIVw+F+I+G4 -4381.920 8819.839 - 4.48e-61 8821.959 - 1.86e-61 8950.833 - 5.84e-81
mtREV+I+G4 -4448.758 8915.516 - 7.51e-82 8915.745 - 8e-82 8957.621 - 1.96e-82
mtREV+G4 -4452.789 8921.578 - 3.62e-83 8921.762 - 3.95e-83 8959.005 - 9.81e-83
HIVw+F+G4 -4389.607 8833.215 - 5.58e-64 8835.186 - 2.49e-64 8959.530 - 7.55e-83
mtMet+I+G4 -4462.631 8943.263 - 7.09e-88 8943.492 - 7.55e-88 8985.368 - 1.85e-88
mtMet+G4 -4468.619 8953.238 - 4.83e-90 8953.421 - 5.27e-90 8990.665 - 1.31e-89
mtMAM+I+G4 -4484.229 8986.458 - 2.96e-97 8986.687 - 3.15e-97 9028.563 - 7.72e-98
mtMAM+G4 -4491.262 8998.525 - 7.08e-100 8998.708 - 7.73e-100 9035.952 - 1.92e-99
mtVer+I+G4 -4491.737 9001.473 - 1.62e-100 9001.703 - 1.73e-100 9043.579 - 4.24e-101
mtVer+G4 -4499.986 9015.973 - 1.15e-103 9016.156 - 1.26e-103 9053.400 - 3.12e-103
mtInv+I+G4 -4497.122 9012.243 - 7.44e-103 9012.473 - 7.92e-103 9054.349 - 1.94e-103
mtInv+G4 -4501.408 9018.816 - 2.78e-104 9018.999 - 3.03e-104 9056.243 - 7.53e-104
AIC, w-AIC : Akaike information criterion scores and weights.
AICc, w-AICc : Corrected AIC scores and weights.
BIC, w-BIC : Bayesian information criterion scores and weights.
Plus signs denote the 95% confidence sets.
Minus signs denote significant exclusion.
SUBSTITUTION PROCESS
--------------------
Model of substitution: cpREV+G4
State frequencies: (model)
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 0.2552
Category Relative_rate Proportion
1 0.0024 0.2500
2 0.0705 0.2500
3 0.5124 0.2500
4 3.4148 0.2500
Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category.
MAXIMUM LIKELIHOOD TREE
-----------------------
Log-likelihood of the tree: -4264.2348 (s.e. 105.6605)
Unconstrained log-likelihood (without tree): -3328.5904
Number of free parameters (#branches + #model parameters): 8
Akaike information criterion (AIC) score: 8544.4696
Corrected Akaike information criterion (AICc) score: 8544.6528
Bayesian information criterion (BIC) score: 8581.8963
Total tree length (sum of branch lengths): 0.6566
Sum of internal branch lengths: 0.1265 (19.2602% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'Avrainvillea_mazei_HV02664' is drawn at root
Numbers in parentheses are ultrafast bootstrap support (%)
+---------------------------------------------Avrainvillea_mazei_HV02664
|
+-----------------------------------Bryopsis_plumosa_WEST4718
|
| +----------------------------------Caulerpa_cliftonii_HV03798
+-----------------------| (100)
| +-----------------------Chlorodesmis_fastigiata_HV03865
+---------| (93)
+-----Flabellia_petiolata_HV01202
Tree in newick format:
(Avrainvillea_mazei_HV02664:0.1661897690,Bryopsis_plumosa_WEST4718:0.1298038579,(Caulerpa_cliftonii_HV03798:0.1248392241,(Chlorodesmis_fastigiata_HV03865:0.0854630913,Flabellia_petiolata_HV01202:0.0238380002)93:0.0387725358)100:0.0876893201);
CONSENSUS TREE
--------------
Consensus tree is constructed from 1000 bootstrap trees
Log-likelihood of consensus tree: -4264.234814
Robinson-Foulds distance between ML tree and consensus tree: 0
Branches with support >0.000000% are kept (extended consensus)
Branch lengths are optimized by maximum likelihood on original alignment
Numbers in parentheses are bootstrap supports (%)
+---------------------------------------------Avrainvillea_mazei_HV02664
|
+-----------------------------------Bryopsis_plumosa_WEST4718
|
| +----------------------------------Caulerpa_cliftonii_HV03798
+-----------------------| (100)
| +-----------------------Chlorodesmis_fastigiata_HV03865
+---------| (93)
+-----Flabellia_petiolata_HV01202
Consensus tree in newick format:
(Avrainvillea_mazei_HV02664:0.1661857555,Bryopsis_plumosa_WEST4718:0.1298019354,(Caulerpa_cliftonii_HV03798:0.1248533989,(Chlorodesmis_fastigiata_HV03865:0.0854959744,Flabellia_petiolata_HV01202:0.0237923437)93:0.0387594158)100:0.0876886082);
TIME STAMP
----------
Date and time: Mon Oct 2 04:09:41 2023
Total CPU time used: 2.49664 seconds (0h:0m:2s)
Total wall-clock time used: 2.527305178 seconds (0h:0m:2s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Linux 64-bit built Aug 2 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: herbairumphylo (AVX512, FMA3, 283 GB RAM)
Command: iqtree2 -s results/supermatrix/supermatrix.protein.fa -bb 1000 -m TEST -nt 1 -redo
Seed: 310712 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Oct 2 04:09:36 2023
Kernel: AVX+FMA - 1 threads (32 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 32 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file results/supermatrix/supermatrix.protein.fa ... Fasta format detected
Reading fasta file: done in 9.99868e-05 secs using 98.01% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.000666879 secs using 99.87% CPU
Alignment has 5 sequences with 795 columns, 233 distinct patterns
59 parsimony-informative, 168 singleton sites, 568 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 9.62615e-06 secs using 83.11% CPU
1 Avrainvillea_mazei_HV02664 1.01% passed 99.95%
2 Bryopsis_plumosa_WEST4718 0.38% passed 100.00%
3 Caulerpa_cliftonii_HV03798 0.88% passed 100.00%
4 Chlorodesmis_fastigiata_HV03865 1.38% passed 100.00%
5 Flabellia_petiolata_HV01202 2.26% passed 100.00%
**** TOTAL 1.18% 0 sequences failed composition chi2 test (p-value<5%; df=19)
Checking for duplicate sequences: done in 1.9744e-05 secs using 96.23% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Perform fast likelihood tree search using LG+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.00646721 secs using 99.93% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -4263.611
Optimal log-likelihood: -4263.607
Proportion of invariable sites: 0.358
Gamma shape alpha: 0.536
Parameters optimization took 1 rounds (0.007 sec)
Time for fast ML tree search: 0.041 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 224 protein models (sample size: 795) ...
No. Model -LnL df AIC AICc BIC
1 LG 4378.052 7 8770.104 8770.246 8802.852
2 LG+I 4274.116 8 8564.233 8564.416 8601.659
3 LG+G4 4266.340 8 8548.680 8548.863 8586.107
4 LG+I+G4 4263.605 9 8545.210 8545.439 8587.315
7 LG+F+G4 4249.084 27 8552.168 8554.139 8678.483
8 LG+F+I+G4 4246.511 28 8549.022 8551.142 8680.016
11 WAG+G4 4276.694 8 8569.388 8569.572 8606.815
12 WAG+I+G4 4275.346 9 8568.692 8568.921 8610.797
15 WAG+F+G4 4253.474 27 8560.948 8562.919 8687.263
16 WAG+F+I+G4 4252.112 28 8560.224 8562.344 8691.217
19 JTT+G4 4290.924 8 8597.849 8598.032 8635.275
20 JTT+I+G4 4288.113 9 8594.227 8594.456 8636.332
23 JTT+F+G4 4273.601 27 8601.202 8603.173 8727.517
24 JTT+F+I+G4 4270.827 28 8597.654 8599.774 8728.647
WARNING: Normalizing state frequencies so that sum of them equals to 1
27 Q.pfam+G4 4274.081 8 8564.163 8564.346 8601.590
WARNING: Normalizing state frequencies so that sum of them equals to 1
28 Q.pfam+I+G4 4271.452 9 8560.904 8561.133 8603.009
WARNING: Normalizing state frequencies so that sum of them equals to 1
31 Q.pfam+F+G4 4253.010 27 8560.020 8561.991 8686.335
WARNING: Normalizing state frequencies so that sum of them equals to 1
32 Q.pfam+F+I+G4 4250.465 28 8556.930 8559.050 8687.924
WARNING: Normalizing state frequencies so that sum of them equals to 1
35 Q.bird+G4 4352.531 8 8721.063 8721.246 8758.490
WARNING: Normalizing state frequencies so that sum of them equals to 1
36 Q.bird+I+G4 4345.555 9 8709.110 8709.339 8751.215
WARNING: Normalizing state frequencies so that sum of them equals to 1
39 Q.bird+F+G4 4318.788 27 8691.576 8693.547 8817.891
WARNING: Normalizing state frequencies so that sum of them equals to 1
40 Q.bird+F+I+G4 4311.654 28 8679.308 8681.428 8810.302
WARNING: Normalizing state frequencies so that sum of them equals to 1
43 Q.mammal+G4 4350.388 8 8716.777 8716.960 8754.204
WARNING: Normalizing state frequencies so that sum of them equals to 1
44 Q.mammal+I+G4 4344.882 9 8707.764 8707.993 8749.869
WARNING: Normalizing state frequencies so that sum of them equals to 1
47 Q.mammal+F+G4 4307.577 27 8669.153 8671.124 8795.468
WARNING: Normalizing state frequencies so that sum of them equals to 1
48 Q.mammal+F+I+G4 4302.004 28 8660.008 8662.128 8791.002
51 Q.insect+G4 4303.627 8 8623.254 8623.437 8660.681
52 Q.insect+I+G4 4299.971 9 8617.941 8618.171 8660.046
55 Q.insect+F+G4 4268.562 27 8591.124 8593.095 8717.439
56 Q.insect+F+I+G4 4265.282 28 8586.563 8588.683 8717.557
WARNING: Normalizing state frequencies so that sum of them equals to 1
59 Q.plant+G4 4291.377 8 8598.753 8598.937 8636.180
WARNING: Normalizing state frequencies so that sum of them equals to 1
60 Q.plant+I+G4 4286.649 9 8591.299 8591.528 8633.404
WARNING: Normalizing state frequencies so that sum of them equals to 1
63 Q.plant+F+G4 4266.457 27 8586.915 8588.886 8713.230
WARNING: Normalizing state frequencies so that sum of them equals to 1
64 Q.plant+F+I+G4 4261.841 28 8579.682 8581.802 8710.676
WARNING: Normalizing state frequencies so that sum of them equals to 1
67 Q.yeast+G4 4296.496 8 8608.992 8609.175 8646.419
WARNING: Normalizing state frequencies so that sum of them equals to 1
68 Q.yeast+I+G4 4292.732 9 8603.464 8603.693 8645.569
WARNING: Normalizing state frequencies so that sum of them equals to 1
71 Q.yeast+F+G4 4261.964 27 8577.929 8579.900 8704.244
WARNING: Normalizing state frequencies so that sum of them equals to 1
72 Q.yeast+F+I+G4 4258.571 28 8573.141 8575.261 8704.135
75 JTTDCMut+G4 4290.078 8 8596.156 8596.339 8633.583
76 JTTDCMut+I+G4 4287.253 9 8592.507 8592.736 8634.612
79 JTTDCMut+F+G4 4272.902 27 8599.804 8601.775 8726.119
80 JTTDCMut+F+I+G4 4270.101 28 8596.202 8598.322 8727.195
83 DCMut+G4 4313.567 8 8643.135 8643.318 8680.561
84 DCMut+I+G4 4310.984 9 8639.968 8640.197 8682.073
87 DCMut+F+G4 4273.485 27 8600.970 8602.941 8727.285
88 DCMut+F+I+G4 4270.680 28 8597.360 8599.480 8728.353
91 VT+G4 4278.977 8 8573.953 8574.136 8611.380
92 VT+I+G4 4277.863 9 8573.727 8573.956 8615.832
95 VT+F+G4 4267.014 27 8588.028 8589.999 8714.343
96 VT+F+I+G4 4266.007 28 8588.013 8590.133 8719.007
99 PMB+G4 4296.492 8 8608.984 8609.167 8646.411
100 PMB+I+G4 4295.845 9 8609.691 8609.920 8651.796
103 PMB+F+G4 4272.250 27 8598.500 8600.471 8724.815
104 PMB+F+I+G4 4271.626 28 8599.252 8601.372 8730.246
107 Blosum62+G4 4290.417 8 8596.834 8597.017 8634.261
108 Blosum62+I+G4 4289.528 9 8597.055 8597.284 8639.160
111 Blosum62+F+G4 4276.695 27 8607.391 8609.362 8733.706
112 Blosum62+F+I+G4 4275.878 28 8607.755 8609.875 8738.749
115 Dayhoff+G4 4313.542 8 8643.085 8643.268 8680.512
116 Dayhoff+I+G4 4310.935 9 8639.869 8640.099 8681.974
119 Dayhoff+F+G4 4273.453 27 8600.906 8602.878 8727.222
120 Dayhoff+F+I+G4 4270.621 28 8597.242 8599.362 8728.235
123 mtREV+G4 4452.789 8 8921.578 8921.762 8959.005
124 mtREV+I+G4 4448.758 9 8915.516 8915.745 8957.621
127 mtREV+F+G4 4266.466 27 8586.932 8588.903 8713.247
128 mtREV+F+I+G4 4263.923 28 8583.846 8585.966 8714.839
131 mtART+G4 4438.666 8 8893.332 8893.515 8930.759
132 mtART+I+G4 4433.667 9 8885.334 8885.563 8927.439
135 mtART+F+G4 4258.168 27 8570.336 8572.308 8696.652
136 mtART+F+I+G4 4253.942 28 8563.884 8566.004 8694.877
139 mtZOA+G4 4413.222 8 8842.444 8842.627 8879.870
140 mtZOA+I+G4 4408.102 9 8834.205 8834.434 8876.310
143 mtZOA+F+G4 4255.408 27 8564.815 8566.786 8691.130
144 mtZOA+F+I+G4 4251.120 28 8558.239 8560.359 8689.233
147 mtMet+G4 4468.619 8 8953.238 8953.421 8990.665
148 mtMet+I+G4 4462.631 9 8943.263 8943.492 8985.368
151 mtMet+F+G4 4277.978 27 8609.955 8611.927 8736.271
152 mtMet+F+I+G4 4273.719 28 8603.439 8605.559 8734.432
155 mtVer+G4 4499.986 8 9015.973 9016.156 9053.400
156 mtVer+I+G4 4491.737 9 9001.473 9001.703 9043.579
159 mtVer+F+G4 4308.190 27 8670.379 8672.350 8796.694
160 mtVer+F+I+G4 4301.125 28 8658.250 8660.370 8789.243
163 mtInv+G4 4501.408 8 9018.816 9018.999 9056.243
164 mtInv+I+G4 4497.122 9 9012.243 9012.473 9054.349
167 mtInv+F+G4 4257.685 27 8569.369 8571.341 8695.685
168 mtInv+F+I+G4 4254.766 28 8565.531 8567.652 8696.525
171 mtMAM+G4 4491.262 8 8998.525 8998.708 9035.952
172 mtMAM+I+G4 4484.229 9 8986.458 8986.687 9028.563
175 mtMAM+F+G4 4308.475 27 8670.949 8672.921 8797.265
176 mtMAM+F+I+G4 4302.137 28 8660.274 8662.394 8791.268
WARNING: Normalizing state frequencies so that sum of them equals to 1
179 FLAVI+G4 4401.151 8 8818.302 8818.486 8855.729
WARNING: Normalizing state frequencies so that sum of them equals to 1
180 FLAVI+I+G4 4392.585 9 8803.169 8803.398 8845.274
WARNING: Normalizing state frequencies so that sum of them equals to 1
183 FLAVI+F+G4 4343.385 27 8740.771 8742.742 8867.086
WARNING: Normalizing state frequencies so that sum of them equals to 1
184 FLAVI+F+I+G4 4334.743 28 8725.486 8727.607 8856.480
187 HIVb+G4 4337.534 8 8691.069 8691.252 8728.495
188 HIVb+I+G4 4332.623 9 8683.246 8683.475 8725.351
191 HIVb+F+G4 4307.488 27 8668.976 8670.947 8795.291
192 HIVb+F+I+G4 4302.523 28 8661.045 8663.166 8792.039
195 HIVw+G4 4447.382 8 8910.764 8910.947 8948.191
196 HIVw+I+G4 4438.926 9 8895.852 8896.081 8937.957
199 HIVw+F+G4 4389.607 27 8833.215 8835.186 8959.530
200 HIVw+F+I+G4 4381.920 28 8819.839 8821.959 8950.833
203 FLU+G4 4346.657 8 8709.314 8709.497 8746.741
204 FLU+I+G4 4341.240 9 8700.481 8700.710 8742.586
207 FLU+F+G4 4300.960 27 8655.921 8657.892 8782.236
208 FLU+F+I+G4 4295.811 28 8647.622 8649.742 8778.616
211 rtREV+G4 4288.723 8 8593.447 8593.630 8630.874
212 rtREV+I+G4 4286.522 9 8591.044 8591.273 8633.149
215 rtREV+F+G4 4259.244 27 8572.489 8574.460 8698.804
216 rtREV+F+I+G4 4257.099 28 8570.198 8572.318 8701.192
219 cpREV+G4 4264.235 8 8544.470 8544.653 8581.896
220 cpREV+I+G4 4262.935 9 8543.870 8544.100 8585.975
223 cpREV+F+G4 4247.364 27 8548.727 8550.698 8675.042
224 cpREV+F+I+G4 4246.056 28 8548.113 8550.233 8679.106
Akaike Information Criterion: cpREV+I+G4
Corrected Akaike Information Criterion: cpREV+I+G4
Bayesian Information Criterion: cpREV+G4
Best-fit model: cpREV+G4 chosen according to BIC
All model information printed to results/supermatrix/supermatrix.protein.fa.model.gz
CPU time for ModelFinder: 2.530 seconds (0h:0m:2s)
Wall-clock time for ModelFinder: 2.550 seconds (0h:0m:2s)
Generating 1000 samples for ultrafast bootstrap (seed: 310712)...
NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -4264.235
Optimal log-likelihood: -4264.235
Gamma shape alpha: 0.255
Parameters optimization took 1 rounds (0.008 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00366101 secs using 99.97% CPU
Computing ML distances took 0.003710 sec (of wall-clock time) 0.003714 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 3.97936e-05 secs using 95.49% CPU
Constructing RapidNJ tree: done in 3.24026e-05 secs using 95.67% CPU
Computing RapidNJ tree took 0.000122 sec (of wall-clock time) 0.000120 sec (of CPU time)
Log-likelihood of RapidNJ tree: -4264.235
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 99 parsimony trees... 0.024 second
Computing log-likelihood of 4 initial trees ... 0.010 seconds
Current best score: -4264.235
Do NNI search on 5 best initial trees
Optimizing NNI: done in 0.00643805 secs using 99.95% CPU
Optimizing NNI: done in 0.0146128 secs using 99.84% CPU
Optimizing NNI: done in 0.0147135 secs using 99.97% CPU
Optimizing NNI: done in 0.0147399 secs using 99.97% CPU
Optimizing NNI: done in 0.0146393 secs using 99.97% CPU
Finish initializing candidate tree set (5)
Current best tree score: -4264.235 / CPU time: 0.106
Number of iterations: 5
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.0225526 secs using 99.98% CPU
Optimizing NNI: done in 0.0146354 secs using 99.98% CPU
Optimizing NNI: done in 0.0226541 secs using 99.98% CPU
Optimizing NNI: done in 0.014398 secs using 99.97% CPU
Optimizing NNI: done in 0.0222657 secs using 99.98% CPU
Iteration 10 / LogL: -4264.247 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0233306 secs using 99.98% CPU
Optimizing NNI: done in 0.0228337 secs using 99.99% CPU
Optimizing NNI: done in 0.0227362 secs using 82.39% CPU
Optimizing NNI: done in 0.0144051 secs using 99.98% CPU
UPDATE BEST LOG-LIKELIHOOD: -4264.235
Optimizing NNI: done in 0.0144137 secs using 99.97% CPU
Optimizing NNI: done in 0.0230932 secs using 99.99% CPU
Optimizing NNI: done in 0.0147727 secs using 99.98% CPU
Optimizing NNI: done in 0.0227327 secs using 99.99% CPU
Optimizing NNI: done in 0.014368 secs using 99.98% CPU
Optimizing NNI: done in 0.0225869 secs using 99.98% CPU
Iteration 20 / LogL: -4264.247 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0142816 secs using 99.98% CPU
Optimizing NNI: done in 0.0147616 secs using 99.98% CPU
Optimizing NNI: done in 0.0142101 secs using 99.98% CPU
Optimizing NNI: done in 0.014813 secs using 99.98% CPU
Optimizing NNI: done in 0.0145995 secs using 99.98% CPU
Optimizing NNI: done in 0.0142692 secs using 99.98% CPU
Optimizing NNI: done in 0.0233552 secs using 82.81% CPU
Optimizing NNI: done in 0.0147354 secs using 99.98% CPU
Optimizing NNI: done in 0.0237579 secs using 99.87% CPU
Optimizing NNI: done in 0.0236447 secs using 99.93% CPU
Iteration 30 / LogL: -4264.252 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.0236357 secs using 99.98% CPU
Optimizing NNI: done in 0.0236755 secs using 99.99% CPU
Optimizing NNI: done in 0.0237768 secs using 99.98% CPU
Optimizing NNI: done in 0.0149537 secs using 99.82% CPU
Optimizing NNI: done in 0.0230742 secs using 99.98% CPU
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Iteration 50 / LogL: -4264.252 / Time: 0h:0m:1s (0h:0m:1s left)
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Iteration 100 / LogL: -4264.245 / Time: 0h:0m:2s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -4275.593
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 0.00651161 secs using 99.93% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:2s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -4264.235
Optimal log-likelihood: -4264.235
Gamma shape alpha: 0.255
Parameters optimization took 1 rounds (0.010 sec)
BEST SCORE FOUND : -4264.235
Creating bootstrap support values...
Split supports printed to NEXUS file results/supermatrix/supermatrix.protein.fa.splits.nex
Total tree length: 0.657
Total number of iterations: 101
CPU time used for tree search: 2.431 sec (0h:0m:2s)
Wall-clock time used for tree search: 2.443 sec (0h:0m:2s)
Total CPU time used: 2.497 sec (0h:0m:2s)
Total wall-clock time used: 2.511 sec (0h:0m:2s)
Computing bootstrap consensus tree...
Reading input file results/supermatrix/supermatrix.protein.fa.splits.nex...
5 taxa and 9 splits.
Consensus tree written to results/supermatrix/supermatrix.protein.fa.contree
Reading input trees file results/supermatrix/supermatrix.protein.fa.contree
Log-likelihood of consensus tree: -4264.235
Analysis results written to:
IQ-TREE report: results/supermatrix/supermatrix.protein.fa.iqtree
Maximum-likelihood tree: results/supermatrix/supermatrix.protein.fa.treefile
Likelihood distances: results/supermatrix/supermatrix.protein.fa.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/supermatrix/supermatrix.protein.fa.splits.nex
Consensus tree: results/supermatrix/supermatrix.protein.fa.contree
Screen log file: results/supermatrix/supermatrix.protein.fa.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/supermatrix/supermatrix.protein.fa.treefile -m "cpREV+G4{0.255214}" --length 795
Date and Time: Mon Oct 2 04:09:41 2023
Gene Tree
OG0000005
IQ-TREE 2.2.0.3 COVID-edition built Aug 2 2022
Input file name: results/alignment/trimmed_protein/OG0000005.trimmed.protein.alignment.fa
Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates)
Random seed number: 609633
REFERENCES
----------
To cite IQ-TREE please use:
Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf,
Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020)
IQ-TREE 2: New models and efficient methods for phylogenetic inference
in the genomic era. Mol. Biol. Evol., in press.
https://doi.org/10.1093/molbev/msaa015
To cite ModelFinder please use:
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler,
and Lars S Jermiin (2017) ModelFinder: Fast model selection for
accurate phylogenetic estimates. Nature Methods, 14:587–589.
https://doi.org/10.1038/nmeth.4285
Since you used ultrafast bootstrap (UFBoot) please also cite:
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh,
and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap
approximation. Mol. Biol. Evol., 35:518–522.
https://doi.org/10.1093/molbev/msx281
SEQUENCE ALIGNMENT
------------------
Input data: 5 sequences with 475 amino-acid sites
Number of constant sites: 404 (= 85.0526% of all sites)
Number of invariant (constant or ambiguous constant) sites: 404 (= 85.0526% of all sites)
Number of parsimony informative sites: 30
Number of distinct site patterns: 87
ModelFinder
-----------
Best-fit model according to BIC: WAG+I
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
WAG+I -1976.842 3969.685 + 0.52 3969.994 + 0.521 4002.991 + 0.541
WAG+G4 -1977.019 3970.038 + 0.436 3970.347 + 0.436 4003.344 + 0.453
WAG+I+G4 -1978.313 3974.627 - 0.0439 3975.014 - 0.0423 4012.096 - 0.0057
JTT+I -1984.279 3984.557 - 0.000306 3984.867 - 0.000307 4017.864 - 0.000319
JTT+G4 -1984.325 3984.650 - 0.000292 3984.959 - 0.000293 4017.956 - 0.000304
JTT+I+G4 -1985.808 3989.616 - 2.44e-05 3990.003 - 2.35e-05 4027.086 - 3.17e-06
VT+I -1990.269 3996.538 - 7.67e-07 3996.847 - 7.68e-07 4029.844 - 7.97e-07
VT+G4 -1990.381 3996.762 - 6.85e-07 3997.071 - 6.87e-07 4030.068 - 7.13e-07
cpREV+I -1990.814 3997.627 - 4.45e-07 3997.936 - 4.45e-07 4030.934 - 4.63e-07
Blosum62+I -1990.833 3997.666 - 4.36e-07 3997.975 - 4.37e-07 4030.972 - 4.54e-07
cpREV+G4 -1990.914 3997.828 - 4.02e-07 3998.137 - 4.03e-07 4031.135 - 4.18e-07
Blosum62+G4 -1990.956 3997.911 - 3.86e-07 3998.220 - 3.86e-07 4031.218 - 4.01e-07
Dayhoff+I -1991.652 3999.303 - 1.92e-07 3999.612 - 1.93e-07 4032.610 - 2e-07
Dayhoff+G4 -1991.799 3999.598 - 1.66e-07 3999.907 - 1.66e-07 4032.905 - 1.73e-07
VT+I+G4 -1991.812 4001.624 - 6.03e-08 4002.011 - 5.81e-08 4039.094 - 7.82e-09
WAG -1998.499 4010.998 - 5.55e-10 4011.238 - 5.76e-10 4040.142 - 4.63e-09
cpREV+I+G4 -1992.389 4002.777 - 3.39e-08 4003.164 - 3.26e-08 4040.247 - 4.39e-09
Blosum62+I+G4 -1992.440 4002.881 - 3.22e-08 4003.268 - 3.1e-08 4040.351 - 4.17e-09
Dayhoff+I+G4 -1992.866 4003.732 - 2.1e-08 4004.119 - 2.02e-08 4041.202 - 2.73e-09
rtREV+I -2001.714 4019.428 - 8.21e-12 4019.737 - 8.22e-12 4052.734 - 8.54e-12
rtREV+G4 -2001.854 4019.707 - 7.14e-12 4020.016 - 7.15e-12 4053.014 - 7.42e-12
rtREV+I+G4 -2003.171 4024.341 - 7.03e-13 4024.728 - 6.78e-13 4061.811 - 9.13e-14
cpREV+F+I -1967.230 3988.459 - 4.35e-05 3991.842 - 9.38e-06 4100.869 - 3.01e-22
cpREV+F+G4 -1967.473 3988.946 - 3.41e-05 3992.329 - 7.35e-06 4101.356 - 2.36e-22
rtREV+F+I -1967.477 3988.954 - 3.4e-05 3992.336 - 7.33e-06 4101.363 - 2.35e-22
rtREV+F+G4 -1967.694 3989.388 - 2.74e-05 3992.771 - 5.9e-06 4101.798 - 1.89e-22
WAG+F+I -1968.742 3991.483 - 9.6e-06 3994.866 - 2.07e-06 4103.893 - 6.64e-23
WAG+F+G4 -1968.992 3991.984 - 7.47e-06 3995.367 - 1.61e-06 4104.394 - 5.17e-23
cpREV+F+I+G4 -1968.715 3993.430 - 3.63e-06 3997.071 - 6.87e-07 4110.003 - 3.13e-24
rtREV+F+I+G4 -1968.861 3993.722 - 3.13e-06 3997.363 - 5.93e-07 4110.295 - 2.7e-24
WAG+F+I+G4 -1970.228 3996.456 - 7.99e-07 4000.097 - 1.51e-07 4113.029 - 6.89e-25
JTT+F+I -1973.416 4000.831 - 8.96e-08 4004.214 - 1.93e-08 4113.241 - 6.2e-25
JTT+F+G4 -1973.528 4001.056 - 8.01e-08 4004.439 - 1.73e-08 4113.466 - 5.54e-25
VT+F+I -1974.686 4003.372 - 2.52e-08 4006.755 - 5.42e-09 4115.781 - 1.74e-25
VT+F+G4 -1974.892 4003.784 - 2.05e-08 4007.166 - 4.41e-09 4116.193 - 1.42e-25
Dayhoff+F+I -1975.724 4005.447 - 8.91e-09 4008.830 - 1.92e-09 4117.857 - 6.17e-26
Dayhoff+F+G4 -1975.938 4005.877 - 7.19e-09 4009.259 - 1.55e-09 4118.286 - 4.98e-26
mtREV+F+I -1977.569 4009.139 - 1.41e-09 4012.521 - 3.03e-10 4121.548 - 9.74e-27
mtREV+F+G4 -1977.666 4009.332 - 1.28e-09 4012.714 - 2.75e-10 4121.741 - 8.84e-27
JTT+F+I+G4 -1974.910 4005.821 - 7.39e-09 4009.462 - 1.4e-09 4122.394 - 6.38e-27
VT+F+I+G4 -1976.222 4008.443 - 1.99e-09 4012.085 - 3.77e-10 4125.016 - 1.72e-27
Dayhoff+F+I+G4 -1976.925 4009.850 - 9.86e-10 4013.491 - 1.87e-10 4126.423 - 8.51e-28
Blosum62+F+I -1980.081 4014.162 - 1.14e-10 4017.544 - 2.46e-11 4126.571 - 7.9e-28
Blosum62+F+G4 -1980.295 4014.590 - 9.22e-11 4017.973 - 1.99e-11 4127.000 - 6.38e-28
mtREV+F+I+G4 -1978.620 4013.240 - 1.81e-10 4016.881 - 3.43e-11 4129.813 - 1.56e-28
Blosum62+F+I+G4 -1981.678 4019.357 - 8.5e-12 4022.998 - 1.61e-12 4135.929 - 7.34e-30
mtMAM+F+I -1994.739 4043.478 - 4.92e-17 4046.860 - 1.06e-17 4155.887 - 3.4e-34
mtMAM+F+G4 -1994.778 4043.557 - 4.73e-17 4046.939 - 1.02e-17 4155.966 - 3.27e-34
mtMAM+F+I+G4 -1994.772 4045.544 - 1.75e-17 4049.185 - 3.31e-18 4162.117 - 1.51e-35
mtREV+I -2098.944 4213.887 - 4.87e-54 4214.196 - 4.88e-54 4247.194 - 5.07e-54
mtREV+G4 -2098.955 4213.911 - 4.82e-54 4214.220 - 4.82e-54 4247.217 - 5.01e-54
mtREV+I+G4 -2099.936 4217.872 - 6.65e-55 4218.259 - 6.4e-55 4255.341 - 8.62e-56
mtMAM+G4 -2117.719 4251.437 - 3.42e-62 4251.746 - 3.43e-62 4284.744 - 3.56e-62
mtMAM+I -2117.800 4251.599 - 3.15e-62 4251.908 - 3.16e-62 4284.906 - 3.28e-62
mtMAM+I+G4 -2116.491 4250.982 - 4.29e-62 4251.369 - 4.14e-62 4288.452 - 5.57e-63
AIC, w-AIC : Akaike information criterion scores and weights.
AICc, w-AICc : Corrected AIC scores and weights.
BIC, w-BIC : Bayesian information criterion scores and weights.
Plus signs denote the 95% confidence sets.
Minus signs denote significant exclusion.
SUBSTITUTION PROCESS
--------------------
Model of substitution: WAG+I
State frequencies: (model)
Model of rate heterogeneity: Invar
Proportion of invariable sites: 0.7259
Category Relative_rate Proportion
0 0 0.7259
1 3.6483 0.2741
MAXIMUM LIKELIHOOD TREE
-----------------------
Log-likelihood of the tree: -1976.8422 (s.e. 60.4918)
Unconstrained log-likelihood (without tree): -1656.5515
Number of free parameters (#branches + #model parameters): 8
Akaike information criterion (AIC) score: 3969.6844
Corrected Akaike information criterion (AICc) score: 3969.9934
Bayesian information criterion (BIC) score: 4002.9909
Total tree length (sum of branch lengths): 0.2363
Sum of internal branch lengths: 0.0673 (28.4898% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'Caulerpa_cliftonii_HV03798' is drawn at root
Numbers in parentheses are ultrafast bootstrap support (%)
+----------------------Caulerpa_cliftonii_HV03798
|
| +-------------------------Avrainvillea_mazei_HV02664
+------------------------| (98)
| +---------------------------------Bryopsis_plumosa_WEST4718
|
| +-------------------Chlorodesmis_fastigiata_HV03865
+-------------------| (87)
+-------Flabellia_petiolata_HV01202
Tree in newick format:
(Caulerpa_cliftonii_HV03798:0.0348409091,(Avrainvillea_mazei_HV02664:0.0394632024,Bryopsis_plumosa_WEST4718:0.0515166969)98:0.0372351395,(Chlorodesmis_fastigiata_HV03865:0.0306138910,Flabellia_petiolata_HV01202:0.0125454445)87:0.0300868625);
CONSENSUS TREE
--------------
Consensus tree is constructed from 1000 bootstrap trees
Log-likelihood of consensus tree: -1976.842220
Robinson-Foulds distance between ML tree and consensus tree: 0
Branches with support >0.000000% are kept (extended consensus)
Branch lengths are optimized by maximum likelihood on original alignment
Numbers in parentheses are bootstrap supports (%)
+----------------------Caulerpa_cliftonii_HV03798
|
| +-------------------------Avrainvillea_mazei_HV02664
+------------------------| (98)
| +---------------------------------Bryopsis_plumosa_WEST4718
|
| +-------------------Chlorodesmis_fastigiata_HV03865
+-------------------| (87)
+-------Flabellia_petiolata_HV01202
Consensus tree in newick format:
(Caulerpa_cliftonii_HV03798:0.0347767217,(Avrainvillea_mazei_HV02664:0.0394424138,Bryopsis_plumosa_WEST4718:0.0515126560)98:0.0372686269,(Chlorodesmis_fastigiata_HV03865:0.0306386021,Flabellia_petiolata_HV01202:0.0124962389)87:0.0301160048);
TIME STAMP
----------
Date and time: Mon Oct 2 04:09:14 2023
Total CPU time used: 0.739444 seconds (0h:0m:0s)
Total wall-clock time used: 0.7762097195 seconds (0h:0m:0s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Linux 64-bit built Aug 2 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: herbairumphylo (AVX512, FMA3, 283 GB RAM)
Command: iqtree2 -s results/alignment/trimmed_protein/OG0000005.trimmed.protein.alignment.fa -bb 1000 -m TEST -nt 1 -mset mrbayes -pre results/gene_tree/OG0000005/OG0000005.protein -redo
Seed: 609633 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Oct 2 04:09:13 2023
Kernel: AVX+FMA - 1 threads (32 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 32 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file results/alignment/trimmed_protein/OG0000005.trimmed.protein.alignment.fa ... Fasta format detected
Reading fasta file: done in 8.61287e-05 secs
Alignment most likely contains protein sequences
Constructing alignment: done in 0.000463873 secs
Alignment has 5 sequences with 475 columns, 87 distinct patterns
30 parsimony-informative, 41 singleton sites, 404 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 8.13603e-06 secs
1 Caulerpa_cliftonii_HV03798 0.00% passed 100.00%
2 Avrainvillea_mazei_HV02664 0.00% passed 100.00%
3 Chlorodesmis_fastigiata_HV03865 0.00% passed 100.00%
4 Flabellia_petiolata_HV01202 0.00% passed 100.00%
5 Bryopsis_plumosa_WEST4718 0.00% passed 100.00%
**** TOTAL 0.00% 0 sequences failed composition chi2 test (p-value<5%; df=19)
Checking for duplicate sequences: done in 1.77249e-05 secs
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Perform fast likelihood tree search using LG+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.00284951 secs using 99.91% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -1980.327
Optimal log-likelihood: -1980.320
Proportion of invariable sites: 0.424
Gamma shape alpha: 0.458
Parameters optimization took 1 rounds (0.004 sec)
Time for fast ML tree search: 0.016 seconds
NOTE: ModelFinder requires 0 MB RAM!
ModelFinder will test up to 72 protein models (sample size: 475) ...
No. Model -LnL df AIC AICc BIC
1 WAG 1998.499 7 4010.998 4011.238 4040.142
2 WAG+I 1976.842 8 3969.685 3969.994 4002.991
3 WAG+G4 1977.019 8 3970.038 3970.347 4003.344
4 WAG+I+G4 1978.313 9 3974.627 3975.014 4012.096
6 WAG+F+I 1968.742 27 3991.483 3994.866 4103.893
7 WAG+F+G4 1968.992 27 3991.984 3995.367 4104.394
8 WAG+F+I+G4 1970.228 28 3996.456 4000.097 4113.029
10 JTT+I 1984.279 8 3984.557 3984.867 4017.864
11 JTT+G4 1984.325 8 3984.650 3984.959 4017.956
12 JTT+I+G4 1985.808 9 3989.616 3990.003 4027.086
14 JTT+F+I 1973.416 27 4000.831 4004.214 4113.241
15 JTT+F+G4 1973.528 27 4001.056 4004.439 4113.466
16 JTT+F+I+G4 1974.910 28 4005.821 4009.462 4122.394
18 VT+I 1990.269 8 3996.538 3996.847 4029.844
19 VT+G4 1990.381 8 3996.762 3997.071 4030.068
20 VT+I+G4 1991.812 9 4001.624 4002.011 4039.094
22 VT+F+I 1974.686 27 4003.372 4006.755 4115.781
23 VT+F+G4 1974.892 27 4003.784 4007.166 4116.193
24 VT+F+I+G4 1976.222 28 4008.443 4012.085 4125.016
26 Blosum62+I 1990.833 8 3997.666 3997.975 4030.972
27 Blosum62+G4 1990.956 8 3997.911 3998.220 4031.218
28 Blosum62+I+G4 1992.440 9 4002.881 4003.268 4040.351
30 Blosum62+F+I 1980.081 27 4014.162 4017.544 4126.571
31 Blosum62+F+G4 1980.295 27 4014.590 4017.973 4127.000
32 Blosum62+F+I+G4 1981.678 28 4019.357 4022.998 4135.929
34 Dayhoff+I 1991.652 8 3999.303 3999.612 4032.610
35 Dayhoff+G4 1991.799 8 3999.598 3999.907 4032.905
36 Dayhoff+I+G4 1992.866 9 4003.732 4004.119 4041.202
38 Dayhoff+F+I 1975.724 27 4005.447 4008.830 4117.857
39 Dayhoff+F+G4 1975.938 27 4005.877 4009.259 4118.286
40 Dayhoff+F+I+G4 1976.925 28 4009.850 4013.491 4126.423
42 mtREV+I 2098.944 8 4213.887 4214.196 4247.194
43 mtREV+G4 2098.955 8 4213.911 4214.220 4247.217
44 mtREV+I+G4 2099.936 9 4217.872 4218.259 4255.341
46 mtREV+F+I 1977.569 27 4009.139 4012.521 4121.548
47 mtREV+F+G4 1977.666 27 4009.332 4012.714 4121.741
48 mtREV+F+I+G4 1978.620 28 4013.240 4016.881 4129.813
50 mtMAM+I 2117.800 8 4251.599 4251.908 4284.906
51 mtMAM+G4 2117.719 8 4251.437 4251.746 4284.744
52 mtMAM+I+G4 2116.491 9 4250.982 4251.369 4288.452
54 mtMAM+F+I 1994.739 27 4043.478 4046.860 4155.887
55 mtMAM+F+G4 1994.778 27 4043.557 4046.939 4155.966
56 mtMAM+F+I+G4 1994.772 28 4045.544 4049.185 4162.117
58 rtREV+I 2001.714 8 4019.428 4019.737 4052.734
59 rtREV+G4 2001.854 8 4019.707 4020.016 4053.014
60 rtREV+I+G4 2003.171 9 4024.341 4024.728 4061.811
62 rtREV+F+I 1967.477 27 3988.954 3992.336 4101.363
63 rtREV+F+G4 1967.694 27 3989.388 3992.771 4101.798
64 rtREV+F+I+G4 1968.861 28 3993.722 3997.363 4110.295
66 cpREV+I 1990.814 8 3997.627 3997.936 4030.934
67 cpREV+G4 1990.914 8 3997.828 3998.137 4031.135
68 cpREV+I+G4 1992.389 9 4002.777 4003.164 4040.247
70 cpREV+F+I 1967.230 27 3988.459 3991.842 4100.869
71 cpREV+F+G4 1967.473 27 3988.946 3992.329 4101.356
72 cpREV+F+I+G4 1968.715 28 3993.430 3997.071 4110.003
Akaike Information Criterion: WAG+I
Corrected Akaike Information Criterion: WAG+I
Bayesian Information Criterion: WAG+I
Best-fit model: WAG+I chosen according to BIC
All model information printed to results/gene_tree/OG0000005/OG0000005.protein.model.gz
CPU time for ModelFinder: 0.520 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.534 seconds (0h:0m:0s)
Generating 1000 samples for ultrafast bootstrap (seed: 609633)...
NOTE: 0 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -1976.842
Optimal log-likelihood: -1976.842
Proportion of invariable sites: 0.726
Parameters optimization took 1 rounds (0.001 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00106768 secs using 99.94% CPU
Computing ML distances took 0.001113 sec (of wall-clock time) 0.001117 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.24981e-05 secs using 98.83% CPU
Constructing RapidNJ tree: done in 3.41684e-05 secs using 96.58% CPU
Computing RapidNJ tree took 0.000155 sec (of wall-clock time) 0.000154 sec (of CPU time)
Log-likelihood of RapidNJ tree: -1976.842
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| INITIALIZING CANDIDATE TREE SET |
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Generating 99 parsimony trees... 0.014 second
Computing log-likelihood of 4 initial trees ... 0.001 seconds
Current best score: -1976.842
Do NNI search on 5 best initial trees
Optimizing NNI: done in 0.0010382 secs using 95.74% CPU
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Finish initializing candidate tree set (5)
Current best tree score: -1976.842 / CPU time: 0.031
Number of iterations: 5
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| OPTIMIZING CANDIDATE TREE SET |
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UPDATE BEST LOG-LIKELIHOOD: -1976.842
Iteration 10 / LogL: -1976.842 / Time: 0h:0m:0s
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UPDATE BEST LOG-LIKELIHOOD: -1976.842
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Iteration 20 / LogL: -1976.848 / Time: 0h:0m:0s
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Iteration 30 / LogL: -1976.843 / Time: 0h:0m:0s (0h:0m:0s left)
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Iteration 40 / LogL: -1976.873 / Time: 0h:0m:0s (0h:0m:0s left)
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Iteration 50 / LogL: -1976.846 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -2005.231
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Iteration 90 / LogL: -1980.885 / Time: 0h:0m:0s (0h:0m:0s left)
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Iteration 100 / LogL: -1976.885 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -2005.231
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 0.00209629 secs using 99.8% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:0s
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| FINALIZING TREE SEARCH |
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Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -1976.842
Optimal log-likelihood: -1976.842
Proportion of invariable sites: 0.726
Parameters optimization took 1 rounds (0.001 sec)
BEST SCORE FOUND : -1976.842
Creating bootstrap support values...
Split supports printed to NEXUS file results/gene_tree/OG0000005/OG0000005.protein.splits.nex
Total tree length: 0.236
Total number of iterations: 101
CPU time used for tree search: 0.715 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.735 sec (0h:0m:0s)
Total CPU time used: 0.739 sec (0h:0m:0s)
Total wall-clock time used: 0.769 sec (0h:0m:0s)
Computing bootstrap consensus tree...
Reading input file results/gene_tree/OG0000005/OG0000005.protein.splits.nex...
5 taxa and 11 splits.
Consensus tree written to results/gene_tree/OG0000005/OG0000005.protein.contree
Reading input trees file results/gene_tree/OG0000005/OG0000005.protein.contree
Log-likelihood of consensus tree: -1976.842
Analysis results written to:
IQ-TREE report: results/gene_tree/OG0000005/OG0000005.protein.iqtree
Maximum-likelihood tree: results/gene_tree/OG0000005/OG0000005.protein.treefile
Likelihood distances: results/gene_tree/OG0000005/OG0000005.protein.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/gene_tree/OG0000005/OG0000005.protein.splits.nex
Consensus tree: results/gene_tree/OG0000005/OG0000005.protein.contree
Screen log file: results/gene_tree/OG0000005/OG0000005.protein.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/gene_tree/OG0000005/OG0000005.protein.treefile -m "WAG+I{0.725896}" --length 475
Date and Time: Mon Oct 2 04:09:14 2023
OG0000002
IQ-TREE 2.2.0.3 COVID-edition built Aug 2 2022 Input file name: results/alignment/trimmed_protein/OG0000002.trimmed.protein.alignment.fa Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates) Random seed number: 216321 REFERENCES ---------- To cite IQ-TREE please use: Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf, Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., in press. https://doi.org/10.1093/molbev/msaa015 To cite ModelFinder please use: Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler, and Lars S Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14:587–589. https://doi.org/10.1038/nmeth.4285 Since you used ultrafast bootstrap (UFBoot) please also cite: Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281 SEQUENCE ALIGNMENT ------------------ Input data: 5 sequences with 320 amino-acid sites Number of constant sites: 164 (= 51.25% of all sites) Number of invariant (constant or ambiguous constant) sites: 164 (= 51.25% of all sites) Number of parsimony informative sites: 29 Number of distinct site patterns: 169 ModelFinder ----------- Best-fit model according to BIC: WAG+F+G4 List of models sorted by BIC scores: Model LogL AIC w-AIC AICc w-AICc BIC w-BIC WAG+F+G4 -2144.517 4343.034 + 0.759 4348.212 + 0.785 4444.779 + 0.888 cpREV+F+G4 -2147.331 4348.662 - 0.0455 4353.840 - 0.0471 4450.406 + 0.0532 WAG+F+I+G4 -2145.046 4346.092 + 0.165 4351.673 + 0.139 4451.605 - 0.0292 rtREV+F+G4 -2148.671 4351.343 - 0.0119 4356.521 - 0.0123 4453.088 - 0.0139 cpREV+G4 -2204.073 4424.146 - 1.85e-18 4424.609 - 2.02e-17 4454.293 - 0.00763 JTT+F+G4 -2150.533 4355.066 - 0.00185 4360.244 - 0.00191 4456.811 - 0.00216 Dayhoff+F+G4 -2150.632 4355.264 - 0.00168 4360.442 - 0.00173 4457.008 - 0.00196 cpREV+F+I+G4 -2147.753 4351.506 - 0.011 4357.087 - 0.00928 4457.019 - 0.00195 VT+F+G4 -2151.012 4356.024 - 0.00115 4361.202 - 0.00119 4457.768 - 0.00134 rtREV+F+I+G4 -2149.336 4354.672 - 0.00226 4360.253 - 0.00191 4460.185 - 0.000401 cpREV+I+G4 -2204.334 4426.668 - 5.24e-19 4427.249 - 5.4e-18 4460.583 - 0.000328 mtREV+F+G4 -2153.165 4360.330 - 0.000133 4365.508 - 0.000138 4462.075 - 0.000156 JTT+F+I+G4 -2151.136 4358.273 - 0.000373 4363.853 - 0.000315 4463.786 - 6.62e-05 VT+F+I+G4 -2151.594 4359.187 - 0.000236 4364.768 - 0.000199 4464.700 - 4.19e-05 Dayhoff+F+I+G4 -2151.630 4359.260 - 0.000227 4364.841 - 0.000192 4464.773 - 4.04e-05 rtREV+G4 -2210.607 4437.213 - 2.69e-21 4437.676 - 2.94e-20 4467.360 - 1.11e-05 mtREV+F+I+G4 -2153.708 4363.415 - 2.85e-05 4368.996 - 2.41e-05 4468.928 - 5.06e-06 Blosum62+F+G4 -2157.797 4369.594 - 1.3e-06 4374.772 - 1.34e-06 4471.339 - 1.52e-06 rtREV+I+G4 -2211.145 4440.289 - 5.78e-22 4440.870 - 5.95e-21 4474.204 - 3.62e-07 VT+G4 -2215.970 4447.939 - 1.26e-23 4448.402 - 1.38e-22 4478.086 - 5.2e-08 Blosum62+F+I+G4 -2158.368 4372.736 - 2.69e-07 4378.317 - 2.28e-07 4478.249 - 4.79e-08 mtMAM+F+G4 -2163.960 4381.920 - 2.73e-09 4387.098 - 2.82e-09 4483.664 - 3.19e-09 VT+I+G4 -2216.407 4450.815 - 2.99e-24 4451.396 - 3.08e-23 4484.730 - 1.87e-09 mtMAM+F+I+G4 -2165.068 4386.137 - 3.32e-10 4391.717 - 2.8e-10 4491.650 - 5.89e-11 WAG+G4 -2227.497 4470.994 - 1.24e-28 4471.457 - 1.36e-27 4501.141 - 5.12e-13 Blosum62+G4 -2228.352 4472.703 - 5.28e-29 4473.166 - 5.77e-28 4502.850 - 2.18e-13 JTT+G4 -2228.811 4473.621 - 3.34e-29 4474.084 - 3.65e-28 4503.768 - 1.38e-13 WAG+I+G4 -2227.814 4473.628 - 3.33e-29 4474.209 - 3.43e-28 4507.543 - 2.09e-14 Blosum62+I+G4 -2228.829 4475.659 - 1.21e-29 4476.239 - 1.24e-28 4509.574 - 7.55e-15 JTT+I+G4 -2229.296 4476.592 - 7.56e-30 4477.172 - 7.79e-29 4510.507 - 4.74e-15 WAG+I -2236.542 4489.083 - 1.47e-32 4489.546 - 1.6e-31 4519.230 - 6.04e-17 Dayhoff+G4 -2246.730 4509.460 - 5.51e-37 4509.923 - 6.02e-36 4539.606 - 2.27e-21 Dayhoff+I+G4 -2247.249 4512.497 - 1.21e-37 4513.078 - 1.24e-36 4546.412 - 7.56e-23 WAG -2277.653 4569.306 - 5.57e-50 4569.664 - 6.41e-49 4595.684 - 1.51e-33 mtREV+G4 -2280.948 4577.895 - 7.6e-52 4578.358 - 8.3e-51 4608.042 - 3.13e-36 mtREV+I+G4 -2282.280 4582.559 - 7.38e-53 4583.140 - 7.6e-52 4616.474 - 4.62e-38 mtMAM+G4 -2297.666 4611.333 - 4.17e-59 4611.796 - 4.55e-58 4641.479 - 1.72e-43 mtMAM+I+G4 -2299.066 4616.131 - 3.78e-60 4616.712 - 3.9e-59 4650.046 - 2.37e-45 AIC, w-AIC : Akaike information criterion scores and weights. AICc, w-AICc : Corrected AIC scores and weights. BIC, w-BIC : Bayesian information criterion scores and weights. Plus signs denote the 95% confidence sets. Minus signs denote significant exclusion. SUBSTITUTION PROCESS -------------------- Model of substitution: WAG+F+G4 State frequencies: (empirical counts from alignment) pi(A) = 0.0464 pi(R) = 0.0264 pi(N) = 0.0741 pi(D) = 0.0303 pi(C) = 0.0077 pi(Q) = 0.0856 pi(E) = 0.0476 pi(G) = 0.0683 pi(H) = 0.0032 pi(I) = 0.0959 pi(L) = 0.0934 pi(K) = 0.0805 pi(M) = 0.0090 pi(F) = 0.0573 pi(P) = 0.0773 pi(S) = 0.0464 pi(T) = 0.0341 pi(W) = 0.0000 pi(Y) = 0.0367 pi(V) = 0.0798 Model of rate heterogeneity: Gamma with 4 categories Gamma shape alpha: 0.4847 Category Relative_rate Proportion 1 0.0306 0.2500 2 0.2418 0.2500 3 0.8088 0.2500 4 2.9188 0.2500 Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category. MAXIMUM LIKELIHOOD TREE ----------------------- Log-likelihood of the tree: -2144.5170 (s.e. 72.8370) Unconstrained log-likelihood (without tree): -1450.6920 Number of free parameters (#branches + #model parameters): 27 Akaike information criterion (AIC) score: 4343.0340 Corrected Akaike information criterion (AICc) score: 4348.2121 Bayesian information criterion (BIC) score: 4444.7787 Total tree length (sum of branch lengths): 1.4934 Sum of internal branch lengths: 0.2058 (13.7789% of tree length) NOTE: Tree is UNROOTED although outgroup taxon 'Caulerpa_cliftonii_HV03798' is drawn at root Numbers in parentheses are ultrafast bootstrap support (%) +-----------------------------Caulerpa_cliftonii_HV03798 | | +------------------------------------------Avrainvillea_mazei_HV02664 +---------------| (99) | +-------------------------Bryopsis_plumosa_WEST4718 | | +-----------------Chlorodesmis_fastigiata_HV03865 +--| (63) +--Flabellia_petiolata_HV01202 Tree in newick format: (Caulerpa_cliftonii_HV03798:0.3226014898,(Avrainvillea_mazei_HV02664:0.4542202634,Bryopsis_plumosa_WEST4718:0.2769967559)99:0.1710107213,(Chlorodesmis_fastigiata_HV03865:0.1932433340,Flabellia_petiolata_HV01202:0.0405440177)63:0.0347607763); CONSENSUS TREE -------------- Consensus tree is constructed from 1000 bootstrap trees Log-likelihood of consensus tree: -2144.517025 Robinson-Foulds distance between ML tree and consensus tree: 0 Branches with support >0.000000% are kept (extended consensus) Branch lengths are optimized by maximum likelihood on original alignment Numbers in parentheses are bootstrap supports (%) +-----------------------------Caulerpa_cliftonii_HV03798 | | +------------------------------------------Avrainvillea_mazei_HV02664 +---------------| (99) | +-------------------------Bryopsis_plumosa_WEST4718 | | +-----------------Chlorodesmis_fastigiata_HV03865 +--| (63) +--Flabellia_petiolata_HV01202 Consensus tree in newick format: (Caulerpa_cliftonii_HV03798:0.3225589993,(Avrainvillea_mazei_HV02664:0.4541201181,Bryopsis_plumosa_WEST4718:0.2769894668)99:0.1709773967,(Chlorodesmis_fastigiata_HV03865:0.1932260072,Flabellia_petiolata_HV01202:0.0405544450)63:0.0347586722); TIME STAMP ---------- Date and time: Mon Oct 2 04:09:18 2023 Total CPU time used: 2.002328 seconds (0h:0m:2s) Total wall-clock time used: 2.045257002 seconds (0h:0m:2s)
IQ-TREE multicore version 2.2.0.3 COVID-edition for Linux 64-bit built Aug 2 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: herbairumphylo (AVX512, FMA3, 283 GB RAM)
Command: iqtree2 -s results/alignment/trimmed_protein/OG0000002.trimmed.protein.alignment.fa -bb 1000 -m TEST -nt 1 -mset mrbayes -pre results/gene_tree/OG0000002/OG0000002.protein -redo
Seed: 216321 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Mon Oct 2 04:09:15 2023
Kernel: AVX+FMA - 1 threads (32 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 32 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.
Reading alignment file results/alignment/trimmed_protein/OG0000002.trimmed.protein.alignment.fa ... Fasta format detected
Reading fasta file: done in 9.92641e-05 secs using 97.72% CPU
Alignment most likely contains protein sequences
Constructing alignment: done in 0.000360444 secs using 99.88% CPU
Alignment has 5 sequences with 320 columns, 169 distinct patterns
29 parsimony-informative, 127 singleton sites, 164 constant sites
Gap/Ambiguity Composition p-value
Analyzing sequences: done in 9.40263e-06 secs using 85.08% CPU
1 Caulerpa_cliftonii_HV03798 2.19% passed 99.98%
2 Avrainvillea_mazei_HV02664 2.50% passed 97.42%
3 Chlorodesmis_fastigiata_HV03865 3.44% passed 99.98%
4 Flabellia_petiolata_HV01202 5.62% passed 100.00%
5 Bryopsis_plumosa_WEST4718 0.94% passed 99.99%
**** TOTAL 2.94% 0 sequences failed composition chi2 test (p-value<5%; df=19)
Checking for duplicate sequences: done in 2.04518e-05 secs using 92.9% CPU
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
Perform fast likelihood tree search using LG+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Optimizing NNI: done in 0.00496516 secs using 98.26% CPU
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -2210.381
Optimal log-likelihood: -2210.332
Proportion of invariable sites: 0.236
Gamma shape alpha: 0.803
Parameters optimization took 1 rounds (0.007 sec)
Time for fast ML tree search: 0.039 seconds
NOTE: ModelFinder requires 1 MB RAM!
ModelFinder will test up to 72 protein models (sample size: 320) ...
No. Model -LnL df AIC AICc BIC
1 WAG 2277.653 7 4569.306 4569.664 4595.684
2 WAG+I 2236.542 8 4489.083 4489.546 4519.230
3 WAG+G4 2227.497 8 4470.994 4471.457 4501.141
4 WAG+I+G4 2227.814 9 4473.628 4474.209 4507.543
7 WAG+F+G4 2144.517 27 4343.034 4348.212 4444.779
8 WAG+F+I+G4 2145.046 28 4346.092 4351.673 4451.605
11 JTT+G4 2228.811 8 4473.621 4474.084 4503.768
12 JTT+I+G4 2229.296 9 4476.592 4477.172 4510.507
15 JTT+F+G4 2150.533 27 4355.066 4360.244 4456.811
16 JTT+F+I+G4 2151.136 28 4358.273 4363.853 4463.786
19 VT+G4 2215.970 8 4447.939 4448.402 4478.086
20 VT+I+G4 2216.407 9 4450.815 4451.396 4484.730
23 VT+F+G4 2151.012 27 4356.024 4361.202 4457.768
24 VT+F+I+G4 2151.594 28 4359.187 4364.768 4464.700
27 Blosum62+G4 2228.352 8 4472.703 4473.166 4502.850
28 Blosum62+I+G4 2228.829 9 4475.659 4476.239 4509.574
31 Blosum62+F+G4 2157.797 27 4369.594 4374.772 4471.339
32 Blosum62+F+I+G4 2158.368 28 4372.736 4378.317 4478.249
35 Dayhoff+G4 2246.730 8 4509.460 4509.923 4539.606
36 Dayhoff+I+G4 2247.249 9 4512.497 4513.078 4546.412
39 Dayhoff+F+G4 2150.632 27 4355.263 4360.442 4457.008
40 Dayhoff+F+I+G4 2151.630 28 4359.260 4364.841 4464.773
43 mtREV+G4 2280.948 8 4577.895 4578.358 4608.042
44 mtREV+I+G4 2282.280 9 4582.559 4583.140 4616.474
47 mtREV+F+G4 2153.165 27 4360.330 4365.508 4462.075
48 mtREV+F+I+G4 2153.708 28 4363.415 4368.996 4468.928
51 mtMAM+G4 2297.666 8 4611.333 4611.796 4641.479
52 mtMAM+I+G4 2299.066 9 4616.131 4616.712 4650.046
55 mtMAM+F+G4 2163.960 27 4381.920 4387.098 4483.664
56 mtMAM+F+I+G4 2165.068 28 4386.137 4391.717 4491.650
59 rtREV+G4 2210.607 8 4437.213 4437.676 4467.360
60 rtREV+I+G4 2211.145 9 4440.289 4440.870 4474.204
63 rtREV+F+G4 2148.671 27 4351.343 4356.521 4453.088
64 rtREV+F+I+G4 2149.336 28 4354.672 4360.253 4460.185
67 cpREV+G4 2204.073 8 4424.146 4424.609 4454.293
68 cpREV+I+G4 2204.334 9 4426.668 4427.249 4460.583
71 cpREV+F+G4 2147.331 27 4348.662 4353.840 4450.406
72 cpREV+F+I+G4 2147.753 28 4351.506 4357.087 4457.019
Akaike Information Criterion: WAG+F+G4
Corrected Akaike Information Criterion: WAG+F+G4
Bayesian Information Criterion: WAG+F+G4
Best-fit model: WAG+F+G4 chosen according to BIC
All model information printed to results/gene_tree/OG0000002/OG0000002.protein.model.gz
CPU time for ModelFinder: 0.795 seconds (0h:0m:0s)
Wall-clock time for ModelFinder: 0.811 seconds (0h:0m:0s)
WARNING: States(s) W rarely appear in alignment and may cause numerical problems
Generating 1000 samples for ultrafast bootstrap (seed: 216321)...
NOTE: 1 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -2144.517
Optimal log-likelihood: -2144.517
Gamma shape alpha: 0.485
Parameters optimization took 1 rounds (0.005 sec)
Wrote distance file to...
Computing ML distances based on estimated model parameters...
Calculating distance matrix: done in 0.00364403 secs using 99.67% CPU
Computing ML distances took 0.003709 sec (of wall-clock time) 0.003702 sec (of CPU time)
Setting up auxiliary I and S matrices: done in 4.15519e-05 secs using 96.27% CPU
Constructing RapidNJ tree: done in 3.33339e-05 secs using 99% CPU
Computing RapidNJ tree took 0.000149 sec (of wall-clock time) 0.000148 sec (of CPU time)
Log-likelihood of RapidNJ tree: -2144.517
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 99 parsimony trees... 0.019 second
Computing log-likelihood of 4 initial trees ... 0.008 seconds
Current best score: -2144.517
Do NNI search on 5 best initial trees
Optimizing NNI: done in 0.00548873 secs using 99.88% CPU
Optimizing NNI: done in 0.0120553 secs using 99.96% CPU
Optimizing NNI: done in 0.0117353 secs using 99.96% CPU
Optimizing NNI: done in 0.012118 secs using 99.95% CPU
Optimizing NNI: done in 0.0117098 secs using 99.92% CPU
Finish initializing candidate tree set (5)
Current best tree score: -2144.517 / CPU time: 0.088
Number of iterations: 5
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Optimizing NNI: done in 0.00517675 secs using 99.91% CPU
Optimizing NNI: done in 0.0177105 secs using 77.69% CPU
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Optimizing NNI: done in 0.0176273 secs using 99.98% CPU
Optimizing NNI: done in 0.0117142 secs using 99.96% CPU
Iteration 10 / LogL: -2144.549 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0179649 secs using 99.88% CPU
Optimizing NNI: done in 0.0117561 secs using 99.97% CPU
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Optimizing NNI: done in 0.0179775 secs using 99.69% CPU
Optimizing NNI: done in 0.0110446 secs using 99.97% CPU
UPDATE BEST LOG-LIKELIHOOD: -2144.517
Optimizing NNI: done in 0.0118003 secs using 99.96% CPU
Optimizing NNI: done in 0.011216 secs using 99.96% CPU
UPDATE BEST LOG-LIKELIHOOD: -2144.517
Optimizing NNI: done in 0.0181741 secs using 99.98% CPU
Iteration 20 / LogL: -2144.518 / Time: 0h:0m:0s
Optimizing NNI: done in 0.0183964 secs using 99.95% CPU
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Optimizing NNI: done in 0.0116064 secs using 99.97% CPU
Optimizing NNI: done in 0.0173832 secs using 99.68% CPU
Iteration 30 / LogL: -2144.858 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.0179739 secs using 99.98% CPU
Optimizing NNI: done in 0.0175836 secs using 99.99% CPU
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Optimizing NNI: done in 0.017407 secs using 99.98% CPU
Optimizing NNI: done in 0.0175627 secs using 99.98% CPU
Optimizing NNI: done in 0.0112698 secs using 99.97% CPU
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Optimizing NNI: done in 0.0113202 secs using 99.96% CPU
Optimizing NNI: done in 0.0113288 secs using 99.97% CPU
Iteration 40 / LogL: -2144.559 / Time: 0h:0m:0s (0h:0m:1s left)
Optimizing NNI: done in 0.0111446 secs using 99.34% CPU
Optimizing NNI: done in 0.0116282 secs using 99.96% CPU
Optimizing NNI: done in 0.0110565 secs using 99.97% CPU
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Optimizing NNI: done in 0.00509244 secs using 99.93% CPU
Optimizing NNI: done in 0.0117433 secs using 99.96% CPU
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Optimizing NNI: done in 0.0182306 secs using 99.98% CPU
Optimizing NNI: done in 0.0180713 secs using 99.98% CPU
Iteration 50 / LogL: -2144.858 / Time: 0h:0m:0s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -2161.422
Optimizing NNI: done in 0.0175466 secs using 99.67% CPU
Optimizing NNI: done in 0.018185 secs using 99.98% CPU
Optimizing NNI: done in 0.0178367 secs using 99.93% CPU
Optimizing NNI: done in 0.0174036 secs using 99.99% CPU
Optimizing NNI: done in 0.0175912 secs using 99.98% CPU
Optimizing NNI: done in 0.011045 secs using 99.97% CPU
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Optimizing NNI: done in 0.0117036 secs using 99.98% CPU
Optimizing NNI: done in 0.018299 secs using 99.98% CPU
Iteration 60 / LogL: -2144.526 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.01167 secs using 99.97% CPU
Optimizing NNI: done in 0.011448 secs using 99.97% CPU
Optimizing NNI: done in 0.0180985 secs using 99.93% CPU
Optimizing NNI: done in 0.0114473 secs using 99.96% CPU
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Optimizing NNI: done in 0.0117514 secs using 99.97% CPU
Optimizing NNI: done in 0.0116678 secs using 99.98% CPU
Iteration 70 / LogL: -2144.518 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0177888 secs using 99.98% CPU
Optimizing NNI: done in 0.0180905 secs using 99.98% CPU
Optimizing NNI: done in 0.0180416 secs using 99.99% CPU
Optimizing NNI: done in 0.0118398 secs using 99.97% CPU
Optimizing NNI: done in 0.0180478 secs using 99.98% CPU
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Optimizing NNI: done in 0.011672 secs using 99.97% CPU
Optimizing NNI: done in 0.0179876 secs using 99.99% CPU
Optimizing NNI: done in 0.018127 secs using 99.98% CPU
Optimizing NNI: done in 0.0115676 secs using 99.98% CPU
Iteration 80 / LogL: -2144.559 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.00514293 secs using 99.92% CPU
Optimizing NNI: done in 0.0115701 secs using 99.96% CPU
Optimizing NNI: done in 0.0120903 secs using 99.97% CPU
Optimizing NNI: done in 0.0186306 secs using 99.98% CPU
Optimizing NNI: done in 0.019117 secs using 99.98% CPU
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Optimizing NNI: done in 0.0182778 secs using 99.98% CPU
Optimizing NNI: done in 0.0119705 secs using 99.98% CPU
Optimizing NNI: done in 0.0118311 secs using 99.97% CPU
Optimizing NNI: done in 0.0115406 secs using 99.98% CPU
Iteration 90 / LogL: -2144.518 / Time: 0h:0m:1s (0h:0m:0s left)
Optimizing NNI: done in 0.0180666 secs using 99.99% CPU
Optimizing NNI: done in 0.0180573 secs using 99.98% CPU
Optimizing NNI: done in 0.0178148 secs using 99.98% CPU
Optimizing NNI: done in 0.0182629 secs using 99.98% CPU
Optimizing NNI: done in 0.0183802 secs using 78.49% CPU
Optimizing NNI: done in 0.0176956 secs using 99.83% CPU
Optimizing NNI: done in 0.0181387 secs using 99.74% CPU
Optimizing NNI: done in 0.0184269 secs using 99.97% CPU
Optimizing NNI: done in 0.0186856 secs using 99.98% CPU
Optimizing NNI: done in 0.018557 secs using 99.98% CPU
Iteration 100 / LogL: -2144.518 / Time: 0h:0m:1s (0h:0m:0s left)
Log-likelihood cutoff on original alignment: -2160.987
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 1.000
Optimizing NNI: done in 0.0179533 secs using 99.98% CPU
TREE SEARCH COMPLETED AFTER 101 ITERATIONS / Time: 0h:0m:2s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -2144.517
Optimal log-likelihood: -2144.517
Gamma shape alpha: 0.485
Parameters optimization took 1 rounds (0.008 sec)
BEST SCORE FOUND : -2144.517
Creating bootstrap support values...
Split supports printed to NEXUS file results/gene_tree/OG0000002/OG0000002.protein.splits.nex
Total tree length: 1.493
Total number of iterations: 101
CPU time used for tree search: 1.946 sec (0h:0m:1s)
Wall-clock time used for tree search: 1.978 sec (0h:0m:1s)
Total CPU time used: 2.002 sec (0h:0m:2s)
Total wall-clock time used: 2.033 sec (0h:0m:2s)
Computing bootstrap consensus tree...
Reading input file results/gene_tree/OG0000002/OG0000002.protein.splits.nex...
5 taxa and 13 splits.
Consensus tree written to results/gene_tree/OG0000002/OG0000002.protein.contree
Reading input trees file results/gene_tree/OG0000002/OG0000002.protein.contree
Log-likelihood of consensus tree: -2144.517
Analysis results written to:
IQ-TREE report: results/gene_tree/OG0000002/OG0000002.protein.iqtree
Maximum-likelihood tree: results/gene_tree/OG0000002/OG0000002.protein.treefile
Likelihood distances: results/gene_tree/OG0000002/OG0000002.protein.mldist
Ultrafast bootstrap approximation results written to:
Split support values: results/gene_tree/OG0000002/OG0000002.protein.splits.nex
Consensus tree: results/gene_tree/OG0000002/OG0000002.protein.contree
Screen log file: results/gene_tree/OG0000002/OG0000002.protein.log
ALISIM COMMAND
--------------
--alisim simulated_MSA -t results/gene_tree/OG0000002/OG0000002.protein.treefile -m "WAG+F+G4{0.484679}" --length 320
Date and Time: Mon Oct 2 04:09:18 2023
Supertree
Workflow
Bibliography
- 1
- Deren A. R. Eaton. Toytree: A minimalist tree visualization and manipulation library for Python. Methods in Ecology and Evolution, 11:187–191, 2020. doi:10.1111/2041-210X.13313.
- 2
- David M. Emms and Steven Kelly. Orthofinder: phylogenetic orthology inference for comparative genomics. Genome Biology, 20(1):238, 2019. URL: https://doi.org/10.1186/s13059-019-1832-y, doi:10.1186/s13059-019-1832-y.
- 3
- Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, and Le Sy Vinh. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular Biology and Evolution, 35(2):518–522, 10 2017. URL: https://doi.org/10.1093/molbev/msx281, arXiv:https://academic.oup.com/mbe/article-pdf/35/2/518/24367824/msx281.pdf, doi:10.1093/molbev/msx281.
- 4
- Subha Kalyaanamoorthy, Bui Quang Minh, Thomas K F Wong, Arndt von Haeseler, and Lars S Jermiin. Modelfinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14(6):587–589, 2017. URL: https://doi.org/10.1038/nmeth.4285, doi:10.1038/nmeth.4285.
- 5
- Kazutaka Katoh and Daron M. Standley. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30(4):772–780, 01 2013. URL: https://doi.org/10.1093/molbev/mst010, arXiv:https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf, doi:10.1093/molbev/mst010.
- 6
- Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, and Robert Lanfear. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution, 37(5):1530–1534, 02 2020. URL: https://doi.org/10.1093/molbev/msaa015, arXiv:https://academic.oup.com/mbe/article-pdf/37/5/1530/33386032/msaa015.pdf, doi:10.1093/molbev/msaa015.
- 7
- Jacob L Steenwyk, III Buida, Thomas J, Abigail L Labella, Yuanning Li, Xing-Xing Shen, and Antonis Rokas. PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics, 37(16):2325–2331, 02 2021. URL: https://doi.org/10.1093/bioinformatics/btab096, arXiv:https://academic.oup.com/bioinformatics/article-pdf/37/16/2325/39948152/btab096.pdf, doi:10.1093/bioinformatics/btab096.
- 8
- Jacob L. Steenwyk, Thomas J. Buida, Carla Gonçalves, Dayna C. Goltz, Grace Morales, Matthew E. Mead, Abigail L. LaBella, Christina M. Chavez, Jonathan E. Schmitz, Maria Hadjifrangiskou, Yuanning Li, and Antonis Rokas. BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. biorxiv, oct 2021. URL: https://doi.org/10.1101%2F2021.10.02.462868, doi:10.1101/2021.10.02.462868.
- 9
- Jacob L. Steenwyk, Thomas J. Buida, III, Yuanning Li, Xing-Xing Shen, and Antonis Rokas. Clipkit: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLOS Biology, 18(12):1–17, 12 2020. URL: https://doi.org/10.1371/journal.pbio.3001007, doi:10.1371/journal.pbio.3001007.
- 10
- Chao Zhang, Maryam Rabiee, Erfan Sayyari, and Siavash Mirarab. Astral-iii: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19(6):153, 2018. URL: https://doi.org/10.1186/s12859-018-2129-y, doi:10.1186/s12859-018-2129-y.
@article{10.1093/molbev/mst010,
author = "Katoh, Kazutaka and Standley, Daron M.",
title = "{MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability}",
journal = "Molecular Biology and Evolution",
volume = "30",
number = "4",
pages = "772-780",
year = "2013",
month = "01",
abstract = "{We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.}",
issn = "0737-4038",
doi = "10.1093/molbev/mst010",
url = "https://doi.org/10.1093/molbev/mst010",
eprint = "https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf"
}
@article{Emms2019,
author = "Emms, David M. and Kelly, Steven",
type = "Journal Article",
title = "OrthoFinder: phylogenetic orthology inference for comparative genomics",
journal = "Genome Biology",
number = "1",
doi = "10.1186/s13059-019-1832-y",
volume = "20",
pages = "238",
url = "https://doi.org/10.1186/s13059-019-1832-y",
year = "2019",
abstract = "Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder.",
isbn = "1474-760X",
DA = "2019/11/14"
}
@article{10.1371/journal.pbio.3001007,
author = "Steenwyk, Jacob L. and Buida, III, Thomas J. and Li, Yuanning and Shen, Xing-Xing and Rokas, Antonis",
doi = "10.1371/journal.pbio.3001007",
journal = "PLOS Biology",
publisher = "Public Library of Science",
title = "ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference",
year = "2020",
month = "12",
volume = "18",
url = "https://doi.org/10.1371/journal.pbio.3001007",
pages = "1-17",
abstract = "Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference. Thus, several different trimming strategies have been developed for identifying and removing these sites prior to phylogenetic inference. However, a recent study reported that doing so can worsen inference, underscoring the need for alternative alignment trimming strategies. Here, we introduce ClipKIT, an alignment trimming software that, rather than identifying and removing putatively phylogenetically uninformative sites, instead aims to identify and retain parsimony-informative sites, which are known to be phylogenetically informative. To test the efficacy of ClipKIT, we examined the accuracy and support of phylogenies inferred from 14 different alignment trimming strategies, including those implemented in ClipKIT, across nearly 140,000 alignments from a broad sampling of evolutionary histories. Phylogenies inferred from ClipKIT-trimmed alignments are accurate, robust, and time saving. Furthermore, ClipKIT consistently outperformed other trimming methods across diverse datasets, suggesting that strategies based on identifying and retaining parsimony-informative sites provide a robust framework for alignment trimming.",
number = "12"
}
@article{Steenwyk_2021,
author = "Steenwyk, Jacob L. and Buida, Thomas J. and Gon{\c{c}}alves, Carla and Goltz, Dayna C. and Morales, Grace and Mead, Matthew E. and LaBella, Abigail L. and Chavez, Christina M. and Schmitz, Jonathan E. and Hadjifrangiskou, Maria and Li, Yuanning and Rokas, Antonis",
doi = "10.1101/2021.10.02.462868",
url = "https://doi.org/10.1101\%2F2021.10.02.462868",
year = "2021",
month = "oct",
journal = "biorxiv",
publisher = "Cold Spring Harbor Laboratory",
title = "{BioKIT}: a versatile toolkit for processing and analyzing diverse types of sequence data"
}
@article{10.1093/molbev/msx281,
author = "Hoang, Diep Thi and Chernomor, Olga and von Haeseler, Arndt and Minh, Bui Quang and Vinh, Le Sy",
title = "{UFBoot2: Improving the Ultrafast Bootstrap Approximation}",
journal = "Molecular Biology and Evolution",
volume = "35",
number = "2",
pages = "518-522",
year = "2017",
month = "10",
abstract = "{The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.}",
issn = "0737-4038",
doi = "10.1093/molbev/msx281",
url = "https://doi.org/10.1093/molbev/msx281",
eprint = "https://academic.oup.com/mbe/article-pdf/35/2/518/24367824/msx281.pdf"
}
@article{10.1093/bioinformatics/btab096,
author = "Steenwyk, Jacob L and Buida, Thomas J, III and Labella, Abigail L and Li, Yuanning and Shen, Xing-Xing and Rokas, Antonis",
title = "{PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data}",
journal = "Bioinformatics",
volume = "37",
number = "16",
pages = "2325-2331",
year = "2021",
month = "02",
abstract = "{Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and processes and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support.To demonstrate the utility of PhyKIT, we detail three use cases: (1) summarizing information content in MSAs and phylogenetic trees for diagnosing potential biases in sequence or tree data; (2) evaluating gene–gene covariation of evolutionary rates to identify functional relationships, including novel ones, among genes and (3) identify lack of resolution events or polytomies in phylogenetic trees, which are suggestive of rapid radiation events or lack of data. We anticipate PhyKIT will be useful for processing, examining and deriving biological meaning from increasingly large phylogenomic datasets.PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT), PyPi (https://pypi.org/project/phykit/) and the Anaconda Cloud (https://anaconda.org/JLSteenwyk/phykit) under the MIT license with extensive documentation and user tutorials (https://jlsteenwyk.com/PhyKIT).Supplementary data are available at Bioinformatics online.}",
issn = "1367-4803",
doi = "10.1093/bioinformatics/btab096",
url = "https://doi.org/10.1093/bioinformatics/btab096",
eprint = "https://academic.oup.com/bioinformatics/article-pdf/37/16/2325/39948152/btab096.pdf"
}
@article{eaton_toytree_2020,
author = "Eaton, Deren A. R.",
title = "Toytree: {A} minimalist tree visualization and manipulation library for {Python}",
volume = "11",
doi = "10.1111/2041-210X.13313",
journal = "Methods in Ecology and Evolution",
year = "2020",
pages = "187--191"
}
@article{10.1093/molbev/msaa015,
author = "Minh, Bui Quang and Schmidt, Heiko A and Chernomor, Olga and Schrempf, Dominik and Woodhams, Michael D and von Haeseler, Arndt and Lanfear, Robert",
title = "{IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era}",
journal = "Molecular Biology and Evolution",
volume = "37",
number = "5",
pages = "1530-1534",
year = "2020",
month = "02",
abstract = "{IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.}",
issn = "0737-4038",
doi = "10.1093/molbev/msaa015",
url = "https://doi.org/10.1093/molbev/msaa015",
eprint = "https://academic.oup.com/mbe/article-pdf/37/5/1530/33386032/msaa015.pdf"
}
@article{Kalyaanamoorthy2017,
author = "Kalyaanamoorthy, Subha and Minh, Bui Quang and Wong, Thomas K F and von Haeseler, Arndt and Jermiin, Lars S",
type = "Journal Article",
title = "ModelFinder: fast model selection for accurate phylogenetic estimates",
journal = "Nature Methods",
number = "6",
doi = "10.1038/nmeth.4285",
volume = "14",
pages = "587--589",
url = "https://doi.org/10.1038/nmeth.4285",
year = "2017",
abstract = "ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates.",
issn = "1548-7105",
DA = "2017/06/01"
}
@article{Zhang2018,
author = "Zhang, Chao and Rabiee, Maryam and Sayyari, Erfan and Mirarab, Siavash",
type = "Journal Article",
title = "ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees",
journal = "BMC Bioinformatics",
number = "6",
doi = "10.1186/s12859-018-2129-y",
volume = "19",
pages = "153",
url = "https://doi.org/10.1186/s12859-018-2129-y",
year = "2018",
abstract = "Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions.",
issn = "1471-2105",
DA = "2018/05/08"
}File(s) not Fasta or Genbank file. Suffix from file 'NC_026795-truncated.txt' is not Fasta or Genbank. File is assumed to be in Fasta format.